Warning: Permanently added '3.85.236.146' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/10066103-epel-10-aarch64 --chroot epel-10-aarch64


Version: 1.6
PID: 21130
Logging PID: 21132
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 10066103,
 'buildroot_pkgs': [],
 'chroot': 'epel-10-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': 'e09d35abfce8fffc295a0fcc8191ba4c17c19afc',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/bcftools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'bcftools',
 'package_version': '1.23-1',
 'project_dirname': 'bioinformatics',
 'project_name': 'bioinformatics',
 'project_owner': 'ron',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/bioinformatics/epel-10-aarch64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ron/bioinformatics--ron',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'ron',
 'tags': [],
 'task_id': '10066103-epel-10-aarch64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/bcftools /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/bcftools', '/var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools'...

Running: git checkout e09d35abfce8fffc295a0fcc8191ba4c17c19afc --

cmd: ['git', 'checkout', 'e09d35abfce8fffc295a0fcc8191ba4c17c19afc', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools
rc: 0
stdout: 
stderr: Note: switching to 'e09d35abfce8fffc295a0fcc8191ba4c17c19afc'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at e09d35a automatic import of bcftools

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading bcftools-1.23.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o bcftools-1.23.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ron/bioinformatics/bcftools/bcftools-1.23.tar.bz2/md5/a33e895594ff53ed68eded2e0b742540/bcftools-1.23.tar.bz2
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 7942k  100 7942k    0     0   201M      0 --:--:-- --:--:-- --:--:--  204M
INFO: Reading stdout from command: md5sum bcftools-1.23.tar.bz2

tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769502044.615196 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.6 starting (python version = 3.14.2, NVR = mock-6.6-1.fc43), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769502044.615196 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools/bcftools.spec)  Config(centos-stream+epel-10-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.6
INFO: Mock Version: 6.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769502044.615196/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using container image: quay.io/centos/centos:stream10
INFO: Pulling image: quay.io/centos/centos:stream10
INFO: Tagging container image as mock-bootstrap-1a8da867-e271-4c6c-8d1a-ab6b94d9364b
INFO: Checking that c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 image matches host's architecture
INFO: Copy content of container c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 to /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769502044.615196/root
INFO: mounting c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 with podman image mount
INFO: image c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 as /var/lib/containers/storage/overlay/1dc01b598e3ff5390652e58589fa7a58a2d5659c6ca2b463aceb2ed08c570660/merged
INFO: umounting image c785a964505697d8f598018f70abee48cc50e8faf9290eec7850d3d9d4cce980 (/var/lib/containers/storage/overlay/1dc01b598e3ff5390652e58589fa7a58a2d5659c6ca2b463aceb2ed08c570660/merged) with podman image umount
INFO: Removing image mock-bootstrap-1a8da867-e271-4c6c-8d1a-ab6b94d9364b
INFO: Package manager dnf4 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf4 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1.1-21.el10.aarch64
  rpm-sequoia-1.9.0.3-1.el10.aarch64
  python3-dnf-4.20.0-19.el10.noarch
  python3-dnf-plugins-core-4.7.0-10.el10.noarch
  yum-4.20.0-19.el10.noarch
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  20 kB/s | 3.5 kB     00:00    
CentOS Stream 10 - BaseOS                        17 MB/s | 9.3 MB     00:00    
CentOS Stream 10 - AppStream                    6.6 MB/s | 3.5 MB     00:00    
CentOS Stream 10 - CRB                          1.2 MB/s | 778 kB     00:00    
CentOS Stream 10 - Extras packages               26 kB/s | 8.3 kB     00:00    
Extra Packages for Enterprise Linux 10 - aarch6  38 MB/s | 6.1 MB     00:00    
Dependencies resolved.
================================================================================
 Package                    Arch    Version                     Repo       Size
================================================================================
Installing:
 bash                       aarch64 5.2.26-6.el10               baseos    1.8 M
 bzip2                      aarch64 1.0.8-25.el10               baseos     54 k
 centos-stream-release      noarch  10.0-19.el10                baseos     30 k
 coreutils                  aarch64 9.5-6.el10                  baseos    1.1 M
 cpio                       aarch64 2.15-3.el10                 baseos    290 k
 diffutils                  aarch64 3.10-8.el10                 baseos    405 k
 epel-rpm-macros            noarch  10-6.el10_2                 epel      8.2 k
 findutils                  aarch64 1:4.10.0-5.el10             baseos    555 k
 gawk                       aarch64 5.3.0-6.el10                baseos    1.1 M
 glibc-minimal-langpack     aarch64 2.39-99.el10                baseos     39 k
 grep                       aarch64 3.11-10.el10                baseos    298 k
 gzip                       aarch64 1.13-3.el10                 baseos    168 k
 info                       aarch64 7.1-6.el10                  baseos    182 k
 patch                      aarch64 2.7.6-26.el10               appstream 130 k
 redhat-rpm-config          noarch  295-1.el10                  appstream  74 k
 rpm-build                  aarch64 4.19.1.1-21.el10            appstream  76 k
 sed                        aarch64 4.9-3.el10                  baseos    316 k
 shadow-utils               aarch64 2:4.15.0-9.el10             baseos    1.3 M
 tar                        aarch64 2:1.35-10.el10              baseos    857 k
 unzip                      aarch64 6.0-69.el10                 baseos    186 k
 util-linux                 aarch64 2.40.2-13.el10              baseos    1.2 M
 which                      aarch64 2.21-44.el10                baseos     42 k
 xz                         aarch64 1:5.6.2-4.el10              baseos    481 k
Installing dependencies:
 alternatives               aarch64 1.30-2.el10                 baseos     41 k
 ansible-srpm-macros        noarch  1-16.1.el10_0               epel       20 k
 audit-libs                 aarch64 4.0.3-5.el10                baseos    129 k
 authselect                 aarch64 1.5.0-8.el10                baseos    144 k
 authselect-libs            aarch64 1.5.0-8.el10                baseos    221 k
 basesystem                 noarch  11-22.el10                  baseos    4.3 k
 binutils                   aarch64 2.41-60.el10                baseos    6.7 M
 binutils-gold              aarch64 2.41-60.el10                baseos    938 k
 bzip2-libs                 aarch64 1.0.8-25.el10               baseos     42 k
 ca-certificates            noarch  2025.2.80_v9.0.305-102.el10 baseos    1.1 M
 centos-gpg-keys            noarch  10.0-19.el10                baseos     26 k
 centos-stream-repos        noarch  10.0-19.el10                baseos     12 k
 coreutils-common           aarch64 9.5-6.el10                  baseos    2.1 M
 cracklib                   aarch64 2.9.11-8.el10               baseos     96 k
 cracklib-dicts             aarch64 2.9.11-8.el10               baseos    3.6 M
 crypto-policies            noarch  20251127-1.git27c2902.el10  baseos     98 k
 curl                       aarch64 8.12.1-4.el10               baseos    214 k
 cyrus-sasl-lib             aarch64 2.1.28-27.el10              baseos    107 k
 debugedit                  aarch64 5.1-8.el10                  appstream  80 k
 dwz                        aarch64 0.16-1.el10                 appstream 137 k
 ed                         aarch64 1.20-5.el10                 baseos     82 k
 efi-srpm-macros            noarch  6-6.el10                    appstream  24 k
 elfutils                   aarch64 0.194-1.el10                baseos    539 k
 elfutils-debuginfod-client aarch64 0.194-1.el10                baseos     42 k
 elfutils-default-yama-scope
                            noarch  0.194-1.el10                baseos    8.3 k
 elfutils-libelf            aarch64 0.194-1.el10                baseos    199 k
 elfutils-libs              aarch64 0.194-1.el10                baseos    263 k
 file                       aarch64 5.45-8.el10                 baseos     49 k
 file-libs                  aarch64 5.45-8.el10                 baseos    762 k
 filesystem                 aarch64 3.18-17.el10                baseos    4.8 M
 fonts-srpm-macros          noarch  1:2.0.5-18.el10             appstream  27 k
 forge-srpm-macros          noarch  0.4.0-6.el10                appstream  21 k
 fpc-srpm-macros            noarch  1.3-7.el10_1                epel      7.8 k
 gdb-minimal                aarch64 16.3-2.el10                 appstream 4.1 M
 gdbm                       aarch64 1:1.23-14.el10              baseos    150 k
 gdbm-libs                  aarch64 1:1.23-14.el10              baseos     56 k
 ghc-srpm-macros            noarch  1.9.2-1.el10_0              epel      9.1 k
 glibc                      aarch64 2.39-99.el10                baseos    1.7 M
 glibc-common               aarch64 2.39-99.el10                baseos    321 k
 glibc-gconv-extra          aarch64 2.39-99.el10                baseos    1.8 M
 gmp                        aarch64 1:6.2.1-12.el10             baseos    268 k
 go-srpm-macros             noarch  3.8.0-1.el10                appstream  27 k
 jansson                    aarch64 2.14-3.el10                 baseos     47 k
 json-c                     aarch64 0.18-3.el10                 baseos     46 k
 kernel-srpm-macros         noarch  1.0-27.el10                 appstream 8.7 k
 keyutils-libs              aarch64 1.6.3-5.el10                baseos     33 k
 krb5-libs                  aarch64 1.21.3-8.el10               baseos    769 k
 libacl                     aarch64 2.3.2-4.el10                baseos     26 k
 libarchive                 aarch64 3.7.7-4.el10                baseos    406 k
 libattr                    aarch64 2.5.2-5.el10                baseos     19 k
 libblkid                   aarch64 2.40.2-13.el10              baseos    123 k
 libbrotli                  aarch64 1.1.0-7.el10                baseos    344 k
 libcap                     aarch64 2.69-7.el10                 baseos     91 k
 libcap-ng                  aarch64 0.8.4-6.el10                baseos     33 k
 libcom_err                 aarch64 1.47.1-5.el10               baseos     26 k
 libcurl                    aarch64 8.12.1-4.el10               baseos    361 k
 libeconf                   aarch64 0.6.2-4.el10                baseos     33 k
 libevent                   aarch64 2.1.12-16.el10              baseos    256 k
 libfdisk                   aarch64 2.40.2-13.el10              baseos    154 k
 libffi                     aarch64 3.4.4-10.el10               baseos     38 k
 libgcc                     aarch64 14.3.1-4.2.el10             baseos    130 k
 libgomp                    aarch64 14.3.1-4.2.el10             baseos    361 k
 libidn2                    aarch64 2.3.7-3.el10                baseos    119 k
 libmount                   aarch64 2.40.2-13.el10              baseos    153 k
 libnghttp2                 aarch64 1.64.0-2.el10               baseos     77 k
 libpkgconf                 aarch64 2.1.0-3.el10                baseos     39 k
 libpsl                     aarch64 0.21.5-6.el10               baseos     65 k
 libpwquality               aarch64 1.4.5-12.el10               baseos    123 k
 libselinux                 aarch64 3.9-3.el10                  baseos     96 k
 libsemanage                aarch64 3.9-2.el10                  baseos    118 k
 libsepol                   aarch64 3.9-1.el10                  baseos    331 k
 libsmartcols               aarch64 2.40.2-13.el10              baseos     82 k
 libssh                     aarch64 0.11.1-3.el10               baseos    231 k
 libssh-config              noarch  0.11.1-3.el10               baseos    8.4 k
 libstdc++                  aarch64 14.3.1-4.2.el10             baseos    871 k
 libtasn1                   aarch64 4.20.0-1.el10               baseos     74 k
 libunistring               aarch64 1.1-10.el10                 baseos    540 k
 libutempter                aarch64 1.2.1-15.el10               baseos     28 k
 libuuid                    aarch64 2.40.2-13.el10              baseos     28 k
 libverto                   aarch64 0.3.2-10.el10               baseos     22 k
 libxcrypt                  aarch64 4.4.36-10.el10              baseos    124 k
 libxml2                    aarch64 2.12.5-9.el10               baseos    673 k
 libzstd                    aarch64 1.5.5-9.el10                baseos    285 k
 lua-libs                   aarch64 5.4.6-7.el10                baseos    130 k
 lua-srpm-macros            noarch  1-15.el10                   appstream 9.8 k
 lz4-libs                   aarch64 1.9.4-8.el10                baseos     68 k
 mpfr                       aarch64 4.2.1-6.el10                baseos    324 k
 ncurses-base               noarch  6.4-14.20240127.el10        baseos    100 k
 ncurses-libs               aarch64 6.4-14.20240127.el10        baseos    330 k
 ocaml-srpm-macros          noarch  10-4.el10                   appstream  10 k
 openblas-srpm-macros       noarch  2-19.el10                   appstream 8.7 k
 openldap                   aarch64 2.6.10-1.el10               baseos    235 k
 openssl-fips-provider      aarch64 1:3.5.1-6.el10              baseos    716 k
 openssl-libs               aarch64 1:3.5.1-6.el10              baseos    2.1 M
 p11-kit                    aarch64 0.26.1-1.el10               baseos    535 k
 p11-kit-trust              aarch64 0.26.1-1.el10               baseos    141 k
 package-notes-srpm-macros  noarch  0.5-13.el10                 appstream  10 k
 pam                        aarch64 1.6.1-9.el10                baseos    589 k
 pam-libs                   aarch64 1.6.1-9.el10                baseos     56 k
 pcre2                      aarch64 10.44-1.el10.3              baseos    227 k
 pcre2-syntax               noarch  10.44-1.el10.3              baseos    151 k
 perl-srpm-macros           noarch  1-57.el10                   appstream 9.5 k
 pkgconf                    aarch64 2.1.0-3.el10                baseos     44 k
 pkgconf-m4                 noarch  2.1.0-3.el10                baseos     15 k
 pkgconf-pkg-config         aarch64 2.1.0-3.el10                baseos     11 k
 popt                       aarch64 1.19-8.el10                 baseos     65 k
 publicsuffix-list-dafsa    noarch  20240107-5.el10             baseos     59 k
 pyproject-srpm-macros      noarch  1.18.5-1.el10               appstream  13 k
 python-srpm-macros         noarch  3.12-11.el10                appstream  22 k
 qt6-srpm-macros            noarch  6.10.1-1.el10               appstream 9.1 k
 readline                   aarch64 8.2-11.el10                 baseos    212 k
 rpm                        aarch64 4.19.1.1-21.el10            baseos    562 k
 rpm-build-libs             aarch64 4.19.1.1-21.el10            baseos     88 k
 rpm-libs                   aarch64 4.19.1.1-21.el10            baseos    298 k
 rpm-sequoia                aarch64 1.9.0.3-1.el10              baseos    902 k
 rust-toolset-srpm-macros   noarch  1.92.0-1.el10               appstream  11 k
 setup                      noarch  2.14.5-7.el10               baseos    153 k
 sqlite-libs                aarch64 3.46.1-5.el10               baseos    730 k
 systemd-libs               aarch64 257-21.el10                 baseos    788 k
 util-linux-core            aarch64 2.40.2-13.el10              baseos    543 k
 xz-libs                    aarch64 1:5.6.2-4.el10              baseos    110 k
 zip                        aarch64 3.0-45.el10                 baseos    264 k
 zlib-ng-compat             aarch64 2.2.3-3.el10                baseos     63 k
 zstd                       aarch64 1.5.5-9.el10                baseos    455 k

Transaction Summary
================================================================================
Install  147 Packages

Total download size: 60 M
Installed size: 215 M
Downloading Packages:
(1/147): audit-libs-4.0.3-5.el10.aarch64.rpm    8.3 MB/s | 129 kB     00:00    
(2/147): alternatives-1.30-2.el10.aarch64.rpm   2.4 MB/s |  41 kB     00:00    
(3/147): authselect-1.5.0-8.el10.aarch64.rpm    8.2 MB/s | 144 kB     00:00    
(4/147): basesystem-11-22.el10.noarch.rpm       1.9 MB/s | 4.3 kB     00:00    
(5/147): authselect-libs-1.5.0-8.el10.aarch64.r  33 MB/s | 221 kB     00:00    
(6/147): bash-5.2.26-6.el10.aarch64.rpm         105 MB/s | 1.8 MB     00:00    
(7/147): binutils-gold-2.41-60.el10.aarch64.rpm  59 MB/s | 938 kB     00:00    
(8/147): binutils-2.41-60.el10.aarch64.rpm      178 MB/s | 6.7 MB     00:00    
(9/147): bzip2-1.0.8-25.el10.aarch64.rpm        2.4 MB/s |  54 kB     00:00    
(10/147): bzip2-libs-1.0.8-25.el10.aarch64.rpm  2.1 MB/s |  42 kB     00:00    
(11/147): centos-gpg-keys-10.0-19.el10.noarch.r 6.9 MB/s |  26 kB     00:00    
(12/147): centos-stream-release-10.0-19.el10.no 7.2 MB/s |  30 kB     00:00    
(13/147): centos-stream-repos-10.0-19.el10.noar 3.1 MB/s |  12 kB     00:00    
(14/147): ca-certificates-2025.2.80_v9.0.305-10 100 MB/s | 1.1 MB     00:00    
(15/147): coreutils-9.5-6.el10.aarch64.rpm       97 MB/s | 1.1 MB     00:00    
(16/147): coreutils-common-9.5-6.el10.aarch64.r 143 MB/s | 2.1 MB     00:00    
(17/147): cpio-2.15-3.el10.aarch64.rpm           21 MB/s | 290 kB     00:00    
(18/147): cracklib-2.9.11-8.el10.aarch64.rpm     10 MB/s |  96 kB     00:00    
(19/147): crypto-policies-20251127-1.git27c2902  22 MB/s |  98 kB     00:00    
(20/147): curl-8.12.1-4.el10.aarch64.rpm         36 MB/s | 214 kB     00:00    
(21/147): cyrus-sasl-lib-2.1.28-27.el10.aarch64  14 MB/s | 107 kB     00:00    
(22/147): diffutils-3.10-8.el10.aarch64.rpm      58 MB/s | 405 kB     00:00    
(23/147): ed-1.20-5.el10.aarch64.rpm             11 MB/s |  82 kB     00:00    
(24/147): cracklib-dicts-2.9.11-8.el10.aarch64. 131 MB/s | 3.6 MB     00:00    
(25/147): elfutils-0.194-1.el10.aarch64.rpm      38 MB/s | 539 kB     00:00    
(26/147): elfutils-debuginfod-client-0.194-1.el 5.1 MB/s |  42 kB     00:00    
(27/147): elfutils-default-yama-scope-0.194-1.e 3.0 MB/s | 8.3 kB     00:00    
(28/147): elfutils-libelf-0.194-1.el10.aarch64.  46 MB/s | 199 kB     00:00    
(29/147): file-5.45-8.el10.aarch64.rpm           15 MB/s |  49 kB     00:00    
(30/147): elfutils-libs-0.194-1.el10.aarch64.rp  45 MB/s | 263 kB     00:00    
(31/147): file-libs-5.45-8.el10.aarch64.rpm     122 MB/s | 762 kB     00:00    
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(34/147): gawk-5.3.0-6.el10.aarch64.rpm          48 MB/s | 1.1 MB     00:00    
(35/147): gdbm-1.23-14.el10.aarch64.rpm         7.7 MB/s | 150 kB     00:00    
(36/147): gdbm-libs-1.23-14.el10.aarch64.rpm    9.3 MB/s |  56 kB     00:00    
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(38/147): glibc-2.39-99.el10.aarch64.rpm        153 MB/s | 1.7 MB     00:00    
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(40/147): glibc-gconv-extra-2.39-99.el10.aarch6 113 MB/s | 1.8 MB     00:00    
(41/147): gmp-6.2.1-12.el10.aarch64.rpm          34 MB/s | 268 kB     00:00    
(42/147): grep-3.11-10.el10.aarch64.rpm          49 MB/s | 298 kB     00:00    
(43/147): gzip-1.13-3.el10.aarch64.rpm           39 MB/s | 168 kB     00:00    
(44/147): info-7.1-6.el10.aarch64.rpm            42 MB/s | 182 kB     00:00    
(45/147): jansson-2.14-3.el10.aarch64.rpm        14 MB/s |  47 kB     00:00    
(46/147): json-c-0.18-3.el10.aarch64.rpm         10 MB/s |  46 kB     00:00    
(47/147): keyutils-libs-1.6.3-5.el10.aarch64.rp 6.8 MB/s |  33 kB     00:00    
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(51/147): libattr-2.5.2-5.el10.aarch64.rpm      4.8 MB/s |  19 kB     00:00    
(52/147): libblkid-2.40.2-13.el10.aarch64.rpm    27 MB/s | 123 kB     00:00    
(53/147): libcap-ng-0.8.4-6.el10.aarch64.rpm     14 MB/s |  33 kB     00:00    
(54/147): libbrotli-1.1.0-7.el10.aarch64.rpm     70 MB/s | 344 kB     00:00    
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(56/147): libcom_err-1.47.1-5.el10.aarch64.rpm   11 MB/s |  26 kB     00:00    
(57/147): libeconf-0.6.2-4.el10.aarch64.rpm      11 MB/s |  33 kB     00:00    
(58/147): libcurl-8.12.1-4.el10.aarch64.rpm      66 MB/s | 361 kB     00:00    
(59/147): libevent-2.1.12-16.el10.aarch64.rpm    48 MB/s | 256 kB     00:00    
(60/147): libffi-3.4.4-10.el10.aarch64.rpm       16 MB/s |  38 kB     00:00    
(61/147): libfdisk-2.40.2-13.el10.aarch64.rpm    29 MB/s | 154 kB     00:00    
(62/147): libgcc-14.3.1-4.2.el10.aarch64.rpm     32 MB/s | 130 kB     00:00    
(63/147): libgomp-14.3.1-4.2.el10.aarch64.rpm    72 MB/s | 361 kB     00:00    
(64/147): libidn2-2.3.7-3.el10.aarch64.rpm       23 MB/s | 119 kB     00:00    
(65/147): libmount-2.40.2-13.el10.aarch64.rpm    32 MB/s | 153 kB     00:00    
(66/147): libpkgconf-2.1.0-3.el10.aarch64.rpm    17 MB/s |  39 kB     00:00    
(67/147): libnghttp2-1.64.0-2.el10.aarch64.rpm   21 MB/s |  77 kB     00:00    
(68/147): libpsl-0.21.5-6.el10.aarch64.rpm       18 MB/s |  65 kB     00:00    
(69/147): libpwquality-1.4.5-12.el10.aarch64.rp  33 MB/s | 123 kB     00:00    
(70/147): libselinux-3.9-3.el10.aarch64.rpm      24 MB/s |  96 kB     00:00    
(71/147): libsemanage-3.9-2.el10.aarch64.rpm     32 MB/s | 118 kB     00:00    
(72/147): libsepol-3.9-1.el10.aarch64.rpm        78 MB/s | 331 kB     00:00    
(73/147): libsmartcols-2.40.2-13.el10.aarch64.r  20 MB/s |  82 kB     00:00    
(74/147): libssh-0.11.1-3.el10.aarch64.rpm       55 MB/s | 231 kB     00:00    
(75/147): libssh-config-0.11.1-3.el10.noarch.rp 3.1 MB/s | 8.4 kB     00:00    
(76/147): libstdc++-14.3.1-4.2.el10.aarch64.rpm 131 MB/s | 871 kB     00:00    
(77/147): libtasn1-4.20.0-1.el10.aarch64.rpm     12 MB/s |  74 kB     00:00    
(78/147): libunistring-1.1-10.el10.aarch64.rpm   77 MB/s | 540 kB     00:00    
(79/147): libutempter-1.2.1-15.el10.aarch64.rpm 7.1 MB/s |  28 kB     00:00    
(80/147): libuuid-2.40.2-13.el10.aarch64.rpm    9.7 MB/s |  28 kB     00:00    
(81/147): libverto-0.3.2-10.el10.aarch64.rpm    7.7 MB/s |  22 kB     00:00    
(82/147): libxcrypt-4.4.36-10.el10.aarch64.rpm   28 MB/s | 124 kB     00:00    
(83/147): libzstd-1.5.5-9.el10.aarch64.rpm       57 MB/s | 285 kB     00:00    
(84/147): libxml2-2.12.5-9.el10.aarch64.rpm      85 MB/s | 673 kB     00:00    
(85/147): lua-libs-5.4.6-7.el10.aarch64.rpm      28 MB/s | 130 kB     00:00    
(86/147): lz4-libs-1.9.4-8.el10.aarch64.rpm      16 MB/s |  68 kB     00:00    
(87/147): mpfr-4.2.1-6.el10.aarch64.rpm          71 MB/s | 324 kB     00:00    
(88/147): ncurses-base-6.4-14.20240127.el10.noa  24 MB/s | 100 kB     00:00    
(89/147): ncurses-libs-6.4-14.20240127.el10.aar  58 MB/s | 330 kB     00:00    
(90/147): openldap-2.6.10-1.el10.aarch64.rpm     40 MB/s | 235 kB     00:00    
(91/147): openssl-fips-provider-3.5.1-6.el10.aa  92 MB/s | 716 kB     00:00    
(92/147): p11-kit-0.26.1-1.el10.aarch64.rpm      80 MB/s | 535 kB     00:00    
(93/147): openssl-libs-3.5.1-6.el10.aarch64.rpm 143 MB/s | 2.1 MB     00:00    
(94/147): p11-kit-trust-0.26.1-1.el10.aarch64.r  13 MB/s | 141 kB     00:00    
(95/147): pam-1.6.1-9.el10.aarch64.rpm           59 MB/s | 589 kB     00:00    
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(97/147): pcre2-10.44-1.el10.3.aarch64.rpm       39 MB/s | 227 kB     00:00    
(98/147): pkgconf-2.1.0-3.el10.aarch64.rpm       16 MB/s |  44 kB     00:00    
(99/147): pcre2-syntax-10.44-1.el10.3.noarch.rp  31 MB/s | 151 kB     00:00    
(100/147): pkgconf-m4-2.1.0-3.el10.noarch.rpm   4.8 MB/s |  15 kB     00:00    
(101/147): pkgconf-pkg-config-2.1.0-3.el10.aarc 4.3 MB/s |  11 kB     00:00    
(102/147): popt-1.19-8.el10.aarch64.rpm          19 MB/s |  65 kB     00:00    
(103/147): publicsuffix-list-dafsa-20240107-5.e  20 MB/s |  59 kB     00:00    
(104/147): readline-8.2-11.el10.aarch64.rpm      55 MB/s | 212 kB     00:00    
(105/147): rpm-build-libs-4.19.1.1-21.el10.aarc  20 MB/s |  88 kB     00:00    
(106/147): rpm-4.19.1.1-21.el10.aarch64.rpm      87 MB/s | 562 kB     00:00    
(107/147): rpm-libs-4.19.1.1-21.el10.aarch64.rp  51 MB/s | 298 kB     00:00    
(108/147): sed-4.9-3.el10.aarch64.rpm            59 MB/s | 316 kB     00:00    
(109/147): rpm-sequoia-1.9.0.3-1.el10.aarch64.r 108 MB/s | 902 kB     00:00    
(110/147): setup-2.14.5-7.el10.noarch.rpm        24 MB/s | 153 kB     00:00    
(111/147): shadow-utils-4.15.0-9.el10.aarch64.r 150 MB/s | 1.3 MB     00:00    
(112/147): sqlite-libs-3.46.1-5.el10.aarch64.rp  76 MB/s | 730 kB     00:00    
(113/147): systemd-libs-257-21.el10.aarch64.rpm  66 MB/s | 788 kB     00:00    
(114/147): tar-1.35-10.el10.aarch64.rpm         105 MB/s | 857 kB     00:00    
(115/147): unzip-6.0-69.el10.aarch64.rpm         26 MB/s | 186 kB     00:00    
(116/147): util-linux-2.40.2-13.el10.aarch64.rp 126 MB/s | 1.2 MB     00:00    
(117/147): which-2.21-44.el10.aarch64.rpm       7.0 MB/s |  42 kB     00:00    
(118/147): util-linux-core-2.40.2-13.el10.aarch  60 MB/s | 543 kB     00:00    
(119/147): xz-libs-5.6.2-4.el10.aarch64.rpm      28 MB/s | 110 kB     00:00    
(120/147): xz-5.6.2-4.el10.aarch64.rpm           79 MB/s | 481 kB     00:00    
(121/147): zip-3.0-45.el10.aarch64.rpm           50 MB/s | 264 kB     00:00    
(122/147): zlib-ng-compat-2.2.3-3.el10.aarch64.  18 MB/s |  63 kB     00:00    
(123/147): zstd-1.5.5-9.el10.aarch64.rpm         73 MB/s | 455 kB     00:00    
(124/147): debugedit-5.1-8.el10.aarch64.rpm      14 MB/s |  80 kB     00:00    
(125/147): dwz-0.16-1.el10.aarch64.rpm           24 MB/s | 137 kB     00:00    
(126/147): efi-srpm-macros-6-6.el10.noarch.rpm  8.1 MB/s |  24 kB     00:00    
(127/147): fonts-srpm-macros-2.0.5-18.el10.noar 8.7 MB/s |  27 kB     00:00    
(128/147): forge-srpm-macros-0.4.0-6.el10.noarc 7.0 MB/s |  21 kB     00:00    
(129/147): kernel-srpm-macros-1.0-27.el10.noarc 3.5 MB/s | 8.7 kB     00:00    
(130/147): go-srpm-macros-3.8.0-1.el10.noarch.r 7.7 MB/s |  27 kB     00:00    
(131/147): lua-srpm-macros-1-15.el10.noarch.rpm 3.0 MB/s | 9.8 kB     00:00    
(132/147): ocaml-srpm-macros-10-4.el10.noarch.r 1.9 MB/s |  10 kB     00:00    
(133/147): openblas-srpm-macros-2-19.el10.noarc 1.6 MB/s | 8.7 kB     00:00    
(134/147): gdb-minimal-16.3-2.el10.aarch64.rpm  209 MB/s | 4.1 MB     00:00    
(135/147): package-notes-srpm-macros-0.5-13.el1 1.0 MB/s |  10 kB     00:00    
(136/147): patch-2.7.6-26.el10.aarch64.rpm       17 MB/s | 130 kB     00:00    
(137/147): perl-srpm-macros-1-57.el10.noarch.rp 3.4 MB/s | 9.5 kB     00:00    
(138/147): pyproject-srpm-macros-1.18.5-1.el10. 4.2 MB/s |  13 kB     00:00    
(139/147): python-srpm-macros-3.12-11.el10.noar 4.6 MB/s |  22 kB     00:00    
(140/147): qt6-srpm-macros-6.10.1-1.el10.noarch 3.1 MB/s | 9.1 kB     00:00    
(141/147): redhat-rpm-config-295-1.el10.noarch.  18 MB/s |  74 kB     00:00    
(142/147): rust-toolset-srpm-macros-1.92.0-1.el 3.3 MB/s |  11 kB     00:00    
(143/147): rpm-build-4.19.1.1-21.el10.aarch64.r  17 MB/s |  76 kB     00:00    
(144/147): ansible-srpm-macros-1-16.1.el10_0.no 2.0 MB/s |  20 kB     00:00    
(145/147): epel-rpm-macros-10-6.el10_2.noarch.r 930 kB/s | 8.2 kB     00:00    
(146/147): fpc-srpm-macros-1.3-7.el10_1.noarch. 897 kB/s | 7.8 kB     00:00    
(147/147): ghc-srpm-macros-1.9.2-1.el10_0.noarc 2.8 MB/s | 9.1 kB     00:00    
--------------------------------------------------------------------------------
Total                                            85 MB/s |  60 MB     00:00     
CentOS Stream 10 - BaseOS                       1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x8483C65D:
 Userid     : "CentOS (CentOS Official Signing Key) <security@centos.org>"
 Fingerprint: 99DB 70FA E1D7 CE22 7FB6 4882 05B5 55B3 8483 C65D
 From       : /usr/share/distribution-gpg-keys/centos/RPM-GPG-KEY-CentOS-Official-SHA256
Key imported successfully
Extra Packages for Enterprise Linux 10 - aarch6 1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xE37ED158:
 Userid     : "Fedora (epel10) <epel@fedoraproject.org>"
 Fingerprint: 7D8D 15CB FC4E 6268 8591 FB26 33D9 8517 E37E D158
 From       : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-10
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-17.el10.aarch64                        1/1 
  Preparing        :                                                        1/1 
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  Installing       : rust-toolset-srpm-macros-1.92.0-1.el10.noarch        5/147 
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  Installing       : setup-2.14.5-7.el10.noarch                          21/147 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.5-7.el10.noarch                          21/147 
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  Installing       : ncurses-libs-6.4-14.20240127.el10.aarch64           28/147 
  Installing       : bash-5.2.26-6.el10.aarch64                          29/147 
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  Installing       : xz-libs-1:5.6.2-4.el10.aarch64                      32/147 
  Installing       : readline-8.2-11.el10.aarch64                        33/147 
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  Installing       : libuuid-2.40.2-13.el10.aarch64                      35/147 
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  Installing       : libacl-2.3.2-4.el10.aarch64                         40/147 
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  Installing       : libsepol-3.9-1.el10.aarch64                         61/147 
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  Installing       : grep-3.11-10.el10.aarch64                           72/147 
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  Installing       : libsemanage-3.9-2.el10.aarch64                      76/147 
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  Installing       : coreutils-9.5-6.el10.aarch64                        86/147 
  Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar    87/147 
  Installing       : ca-certificates-2025.2.80_v9.0.305-102.el10.noar    87/147 
  Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar    87/147 
  Installing       : authselect-libs-1.5.0-8.el10.aarch64                88/147 
  Installing       : gzip-1.13-3.el10.aarch64                            89/147 
  Installing       : cracklib-2.9.11-8.el10.aarch64                      90/147 
  Installing       : cracklib-dicts-2.9.11-8.el10.aarch64                91/147 
  Installing       : libpwquality-1.4.5-12.el10.aarch64                  92/147 
  Installing       : libevent-2.1.12-16.el10.aarch64                     93/147 
  Installing       : rpm-sequoia-1.9.0.3-1.el10.aarch64                  94/147 
  Installing       : zip-3.0-45.el10.aarch64                             95/147 
  Installing       : cyrus-sasl-lib-2.1.28-27.el10.aarch64               96/147 
  Installing       : openldap-2.6.10-1.el10.aarch64                      97/147 
  Installing       : gdbm-1:1.23-14.el10.aarch64                         98/147 
  Installing       : pam-1.6.1-9.el10.aarch64                            99/147 
  Installing       : libfdisk-2.40.2-13.el10.aarch64                    100/147 
  Installing       : libxml2-2.12.5-9.el10.aarch64                      101/147 
  Installing       : libarchive-3.7.7-4.el10.aarch64                    102/147 
  Installing       : bzip2-1.0.8-25.el10.aarch64                        103/147 
  Installing       : sqlite-libs-3.46.1-5.el10.aarch64                  104/147 
  Installing       : rpm-libs-4.19.1.1-21.el10.aarch64                  105/147 
  Installing       : ed-1.20-5.el10.aarch64                             106/147 
  Installing       : patch-2.7.6-26.el10.aarch64                        107/147 
  Installing       : elfutils-default-yama-scope-0.194-1.el10.noarch    108/147 
  Running scriptlet: elfutils-default-yama-scope-0.194-1.el10.noarch    108/147 
  Installing       : cpio-2.15-3.el10.aarch64                           109/147 
  Installing       : diffutils-3.10-8.el10.aarch64                      110/147 
  Installing       : json-c-0.18-3.el10.aarch64                         111/147 
  Installing       : keyutils-libs-1.6.3-5.el10.aarch64                 112/147 
  Installing       : libbrotli-1.1.0-7.el10.aarch64                     113/147 
  Installing       : libcom_err-1.47.1-5.el10.aarch64                   114/147 
  Installing       : libgomp-14.3.1-4.2.el10.aarch64                    115/147 
  Installing       : libnghttp2-1.64.0-2.el10.aarch64                   116/147 
  Installing       : libpkgconf-2.1.0-3.el10.aarch64                    117/147 
  Installing       : pkgconf-2.1.0-3.el10.aarch64                       118/147 
  Installing       : pkgconf-pkg-config-2.1.0-3.el10.aarch64            119/147 
  Installing       : libverto-0.3.2-10.el10.aarch64                     120/147 
  Installing       : krb5-libs-1.21.3-8.el10.aarch64                    121/147 
  Installing       : libssh-0.11.1-3.el10.aarch64                       122/147 
  Installing       : libcurl-8.12.1-4.el10.aarch64                      123/147 
  Installing       : elfutils-libs-0.194-1.el10.aarch64                 124/147 
  Installing       : elfutils-debuginfod-client-0.194-1.el10.aarch64    125/147 
  Installing       : binutils-gold-2.41-60.el10.aarch64                 126/147 
  Running scriptlet: binutils-gold-2.41-60.el10.aarch64                 126/147 
  Installing       : binutils-2.41-60.el10.aarch64                      127/147 
  Running scriptlet: binutils-2.41-60.el10.aarch64                      127/147 
  Installing       : elfutils-0.194-1.el10.aarch64                      128/147 
  Installing       : gdb-minimal-16.3-2.el10.aarch64                    129/147 
  Installing       : debugedit-5.1-8.el10.aarch64                       130/147 
  Installing       : rpm-build-libs-4.19.1.1-21.el10.aarch64            131/147 
  Installing       : curl-8.12.1-4.el10.aarch64                         132/147 
  Running scriptlet: rpm-4.19.1.1-21.el10.aarch64                       133/147 
  Installing       : rpm-4.19.1.1-21.el10.aarch64                       133/147 
  Installing       : efi-srpm-macros-6-6.el10.noarch                    134/147 
  Installing       : lua-srpm-macros-1-15.el10.noarch                   135/147 
  Installing       : fonts-srpm-macros-1:2.0.5-18.el10.noarch           136/147 
  Installing       : forge-srpm-macros-0.4.0-6.el10.noarch              137/147 
  Installing       : go-srpm-macros-3.8.0-1.el10.noarch                 138/147 
  Installing       : python-srpm-macros-3.12-11.el10.noarch             139/147 
  Installing       : redhat-rpm-config-295-1.el10.noarch                140/147 
  Installing       : rpm-build-4.19.1.1-21.el10.aarch64                 141/147 
  Installing       : pyproject-srpm-macros-1.18.5-1.el10.noarch         142/147 
  Installing       : util-linux-2.40.2-13.el10.aarch64                  143/147 
  Running scriptlet: util-linux-2.40.2-13.el10.aarch64                  143/147 
  Installing       : authselect-1.5.0-8.el10.aarch64                    144/147 
  Installing       : which-2.21-44.el10.aarch64                         145/147 
  Installing       : info-7.1-6.el10.aarch64                            146/147 
  Installing       : epel-rpm-macros-10-6.el10_2.noarch                 147/147 
  Running scriptlet: filesystem-3.18-17.el10.aarch64                    147/147 
  Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar   147/147 
  Running scriptlet: authselect-libs-1.5.0-8.el10.aarch64               147/147 
  Running scriptlet: rpm-4.19.1.1-21.el10.aarch64                       147/147 
  Running scriptlet: epel-rpm-macros-10-6.el10_2.noarch                 147/147 

Installed:
  alternatives-1.30-2.el10.aarch64                                              
  ansible-srpm-macros-1-16.1.el10_0.noarch                                      
  audit-libs-4.0.3-5.el10.aarch64                                               
  authselect-1.5.0-8.el10.aarch64                                               
  authselect-libs-1.5.0-8.el10.aarch64                                          
  basesystem-11-22.el10.noarch                                                  
  bash-5.2.26-6.el10.aarch64                                                    
  binutils-2.41-60.el10.aarch64                                                 
  binutils-gold-2.41-60.el10.aarch64                                            
  bzip2-1.0.8-25.el10.aarch64                                                   
  bzip2-libs-1.0.8-25.el10.aarch64                                              
  ca-certificates-2025.2.80_v9.0.305-102.el10.noarch                            
  centos-gpg-keys-10.0-19.el10.noarch                                           
  centos-stream-release-10.0-19.el10.noarch                                     
  centos-stream-repos-10.0-19.el10.noarch                                       
  coreutils-9.5-6.el10.aarch64                                                  
  coreutils-common-9.5-6.el10.aarch64                                           
  cpio-2.15-3.el10.aarch64                                                      
  cracklib-2.9.11-8.el10.aarch64                                                
  cracklib-dicts-2.9.11-8.el10.aarch64                                          
  crypto-policies-20251127-1.git27c2902.el10.noarch                             
  curl-8.12.1-4.el10.aarch64                                                    
  cyrus-sasl-lib-2.1.28-27.el10.aarch64                                         
  debugedit-5.1-8.el10.aarch64                                                  
  diffutils-3.10-8.el10.aarch64                                                 
  dwz-0.16-1.el10.aarch64                                                       
  ed-1.20-5.el10.aarch64                                                        
  efi-srpm-macros-6-6.el10.noarch                                               
  elfutils-0.194-1.el10.aarch64                                                 
  elfutils-debuginfod-client-0.194-1.el10.aarch64                               
  elfutils-default-yama-scope-0.194-1.el10.noarch                               
  elfutils-libelf-0.194-1.el10.aarch64                                          
  elfutils-libs-0.194-1.el10.aarch64                                            
  epel-rpm-macros-10-6.el10_2.noarch                                            
  file-5.45-8.el10.aarch64                                                      
  file-libs-5.45-8.el10.aarch64                                                 
  filesystem-3.18-17.el10.aarch64                                               
  findutils-1:4.10.0-5.el10.aarch64                                             
  fonts-srpm-macros-1:2.0.5-18.el10.noarch                                      
  forge-srpm-macros-0.4.0-6.el10.noarch                                         
  fpc-srpm-macros-1.3-7.el10_1.noarch                                           
  gawk-5.3.0-6.el10.aarch64                                                     
  gdb-minimal-16.3-2.el10.aarch64                                               
  gdbm-1:1.23-14.el10.aarch64                                                   
  gdbm-libs-1:1.23-14.el10.aarch64                                              
  ghc-srpm-macros-1.9.2-1.el10_0.noarch                                         
  glibc-2.39-99.el10.aarch64                                                    
  glibc-common-2.39-99.el10.aarch64                                             
  glibc-gconv-extra-2.39-99.el10.aarch64                                        
  glibc-minimal-langpack-2.39-99.el10.aarch64                                   
  gmp-1:6.2.1-12.el10.aarch64                                                   
  go-srpm-macros-3.8.0-1.el10.noarch                                            
  grep-3.11-10.el10.aarch64                                                     
  gzip-1.13-3.el10.aarch64                                                      
  info-7.1-6.el10.aarch64                                                       
  jansson-2.14-3.el10.aarch64                                                   
  json-c-0.18-3.el10.aarch64                                                    
  kernel-srpm-macros-1.0-27.el10.noarch                                         
  keyutils-libs-1.6.3-5.el10.aarch64                                            
  krb5-libs-1.21.3-8.el10.aarch64                                               
  libacl-2.3.2-4.el10.aarch64                                                   
  libarchive-3.7.7-4.el10.aarch64                                               
  libattr-2.5.2-5.el10.aarch64                                                  
  libblkid-2.40.2-13.el10.aarch64                                               
  libbrotli-1.1.0-7.el10.aarch64                                                
  libcap-2.69-7.el10.aarch64                                                    
  libcap-ng-0.8.4-6.el10.aarch64                                                
  libcom_err-1.47.1-5.el10.aarch64                                              
  libcurl-8.12.1-4.el10.aarch64                                                 
  libeconf-0.6.2-4.el10.aarch64                                                 
  libevent-2.1.12-16.el10.aarch64                                               
  libfdisk-2.40.2-13.el10.aarch64                                               
  libffi-3.4.4-10.el10.aarch64                                                  
  libgcc-14.3.1-4.2.el10.aarch64                                                
  libgomp-14.3.1-4.2.el10.aarch64                                               
  libidn2-2.3.7-3.el10.aarch64                                                  
  libmount-2.40.2-13.el10.aarch64                                               
  libnghttp2-1.64.0-2.el10.aarch64                                              
  libpkgconf-2.1.0-3.el10.aarch64                                               
  libpsl-0.21.5-6.el10.aarch64                                                  
  libpwquality-1.4.5-12.el10.aarch64                                            
  libselinux-3.9-3.el10.aarch64                                                 
  libsemanage-3.9-2.el10.aarch64                                                
  libsepol-3.9-1.el10.aarch64                                                   
  libsmartcols-2.40.2-13.el10.aarch64                                           
  libssh-0.11.1-3.el10.aarch64                                                  
  libssh-config-0.11.1-3.el10.noarch                                            
  libstdc++-14.3.1-4.2.el10.aarch64                                             
  libtasn1-4.20.0-1.el10.aarch64                                                
  libunistring-1.1-10.el10.aarch64                                              
  libutempter-1.2.1-15.el10.aarch64                                             
  libuuid-2.40.2-13.el10.aarch64                                                
  libverto-0.3.2-10.el10.aarch64                                                
  libxcrypt-4.4.36-10.el10.aarch64                                              
  libxml2-2.12.5-9.el10.aarch64                                                 
  libzstd-1.5.5-9.el10.aarch64                                                  
  lua-libs-5.4.6-7.el10.aarch64                                                 
  lua-srpm-macros-1-15.el10.noarch                                              
  lz4-libs-1.9.4-8.el10.aarch64                                                 
  mpfr-4.2.1-6.el10.aarch64                                                     
  ncurses-base-6.4-14.20240127.el10.noarch                                      
  ncurses-libs-6.4-14.20240127.el10.aarch64                                     
  ocaml-srpm-macros-10-4.el10.noarch                                            
  openblas-srpm-macros-2-19.el10.noarch                                         
  openldap-2.6.10-1.el10.aarch64                                                
  openssl-fips-provider-1:3.5.1-6.el10.aarch64                                  
  openssl-libs-1:3.5.1-6.el10.aarch64                                           
  p11-kit-0.26.1-1.el10.aarch64                                                 
  p11-kit-trust-0.26.1-1.el10.aarch64                                           
  package-notes-srpm-macros-0.5-13.el10.noarch                                  
  pam-1.6.1-9.el10.aarch64                                                      
  pam-libs-1.6.1-9.el10.aarch64                                                 
  patch-2.7.6-26.el10.aarch64                                                   
  pcre2-10.44-1.el10.3.aarch64                                                  
  pcre2-syntax-10.44-1.el10.3.noarch                                            
  perl-srpm-macros-1-57.el10.noarch                                             
  pkgconf-2.1.0-3.el10.aarch64                                                  
  pkgconf-m4-2.1.0-3.el10.noarch                                                
  pkgconf-pkg-config-2.1.0-3.el10.aarch64                                       
  popt-1.19-8.el10.aarch64                                                      
  publicsuffix-list-dafsa-20240107-5.el10.noarch                                
  pyproject-srpm-macros-1.18.5-1.el10.noarch                                    
  python-srpm-macros-3.12-11.el10.noarch                                        
  qt6-srpm-macros-6.10.1-1.el10.noarch                                          
  readline-8.2-11.el10.aarch64                                                  
  redhat-rpm-config-295-1.el10.noarch                                           
  rpm-4.19.1.1-21.el10.aarch64                                                  
  rpm-build-4.19.1.1-21.el10.aarch64                                            
  rpm-build-libs-4.19.1.1-21.el10.aarch64                                       
  rpm-libs-4.19.1.1-21.el10.aarch64                                             
  rpm-sequoia-1.9.0.3-1.el10.aarch64                                            
  rust-toolset-srpm-macros-1.92.0-1.el10.noarch                                 
  sed-4.9-3.el10.aarch64                                                        
  setup-2.14.5-7.el10.noarch                                                    
  shadow-utils-2:4.15.0-9.el10.aarch64                                          
  sqlite-libs-3.46.1-5.el10.aarch64                                             
  systemd-libs-257-21.el10.aarch64                                              
  tar-2:1.35-10.el10.aarch64                                                    
  unzip-6.0-69.el10.aarch64                                                     
  util-linux-2.40.2-13.el10.aarch64                                             
  util-linux-core-2.40.2-13.el10.aarch64                                        
  which-2.21-44.el10.aarch64                                                    
  xz-1:5.6.2-4.el10.aarch64                                                     
  xz-libs-1:5.6.2-4.el10.aarch64                                                
  zip-3.0-45.el10.aarch64                                                       
  zlib-ng-compat-2.2.3-3.el10.aarch64                                           
  zstd-1.5.5-9.el10.aarch64                                                     

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.30-2.el10.aarch64
ansible-srpm-macros-1-16.1.el10_0.noarch
audit-libs-4.0.3-5.el10.aarch64
authselect-1.5.0-8.el10.aarch64
authselect-libs-1.5.0-8.el10.aarch64
basesystem-11-22.el10.noarch
bash-5.2.26-6.el10.aarch64
binutils-2.41-60.el10.aarch64
binutils-gold-2.41-60.el10.aarch64
bzip2-1.0.8-25.el10.aarch64
bzip2-libs-1.0.8-25.el10.aarch64
ca-certificates-2025.2.80_v9.0.305-102.el10.noarch
centos-gpg-keys-10.0-19.el10.noarch
centos-stream-release-10.0-19.el10.noarch
centos-stream-repos-10.0-19.el10.noarch
coreutils-9.5-6.el10.aarch64
coreutils-common-9.5-6.el10.aarch64
cpio-2.15-3.el10.aarch64
cracklib-2.9.11-8.el10.aarch64
cracklib-dicts-2.9.11-8.el10.aarch64
crypto-policies-20251127-1.git27c2902.el10.noarch
curl-8.12.1-4.el10.aarch64
cyrus-sasl-lib-2.1.28-27.el10.aarch64
debugedit-5.1-8.el10.aarch64
diffutils-3.10-8.el10.aarch64
dwz-0.16-1.el10.aarch64
ed-1.20-5.el10.aarch64
efi-srpm-macros-6-6.el10.noarch
elfutils-0.194-1.el10.aarch64
elfutils-debuginfod-client-0.194-1.el10.aarch64
elfutils-default-yama-scope-0.194-1.el10.noarch
elfutils-libelf-0.194-1.el10.aarch64
elfutils-libs-0.194-1.el10.aarch64
epel-rpm-macros-10-6.el10_2.noarch
file-5.45-8.el10.aarch64
file-libs-5.45-8.el10.aarch64
filesystem-3.18-17.el10.aarch64
findutils-4.10.0-5.el10.aarch64
fonts-srpm-macros-2.0.5-18.el10.noarch
forge-srpm-macros-0.4.0-6.el10.noarch
fpc-srpm-macros-1.3-7.el10_1.noarch
gawk-5.3.0-6.el10.aarch64
gdb-minimal-16.3-2.el10.aarch64
gdbm-1.23-14.el10.aarch64
gdbm-libs-1.23-14.el10.aarch64
ghc-srpm-macros-1.9.2-1.el10_0.noarch
glibc-2.39-99.el10.aarch64
glibc-common-2.39-99.el10.aarch64
glibc-gconv-extra-2.39-99.el10.aarch64
glibc-minimal-langpack-2.39-99.el10.aarch64
gmp-6.2.1-12.el10.aarch64
go-srpm-macros-3.8.0-1.el10.noarch
gpg-pubkey-8483c65d-5ccc5b19
gpg-pubkey-e37ed158-65785fa9
grep-3.11-10.el10.aarch64
gzip-1.13-3.el10.aarch64
info-7.1-6.el10.aarch64
jansson-2.14-3.el10.aarch64
json-c-0.18-3.el10.aarch64
kernel-srpm-macros-1.0-27.el10.noarch
keyutils-libs-1.6.3-5.el10.aarch64
krb5-libs-1.21.3-8.el10.aarch64
libacl-2.3.2-4.el10.aarch64
libarchive-3.7.7-4.el10.aarch64
libattr-2.5.2-5.el10.aarch64
libblkid-2.40.2-13.el10.aarch64
libbrotli-1.1.0-7.el10.aarch64
libcap-2.69-7.el10.aarch64
libcap-ng-0.8.4-6.el10.aarch64
libcom_err-1.47.1-5.el10.aarch64
libcurl-8.12.1-4.el10.aarch64
libeconf-0.6.2-4.el10.aarch64
libevent-2.1.12-16.el10.aarch64
libfdisk-2.40.2-13.el10.aarch64
libffi-3.4.4-10.el10.aarch64
libgcc-14.3.1-4.2.el10.aarch64
libgomp-14.3.1-4.2.el10.aarch64
libidn2-2.3.7-3.el10.aarch64
libmount-2.40.2-13.el10.aarch64
libnghttp2-1.64.0-2.el10.aarch64
libpkgconf-2.1.0-3.el10.aarch64
libpsl-0.21.5-6.el10.aarch64
libpwquality-1.4.5-12.el10.aarch64
libselinux-3.9-3.el10.aarch64
libsemanage-3.9-2.el10.aarch64
libsepol-3.9-1.el10.aarch64
libsmartcols-2.40.2-13.el10.aarch64
libssh-0.11.1-3.el10.aarch64
libssh-config-0.11.1-3.el10.noarch
libstdc++-14.3.1-4.2.el10.aarch64
libtasn1-4.20.0-1.el10.aarch64
libunistring-1.1-10.el10.aarch64
libutempter-1.2.1-15.el10.aarch64
libuuid-2.40.2-13.el10.aarch64
libverto-0.3.2-10.el10.aarch64
libxcrypt-4.4.36-10.el10.aarch64
libxml2-2.12.5-9.el10.aarch64
libzstd-1.5.5-9.el10.aarch64
lua-libs-5.4.6-7.el10.aarch64
lua-srpm-macros-1-15.el10.noarch
lz4-libs-1.9.4-8.el10.aarch64
mpfr-4.2.1-6.el10.aarch64
ncurses-base-6.4-14.20240127.el10.noarch
ncurses-libs-6.4-14.20240127.el10.aarch64
ocaml-srpm-macros-10-4.el10.noarch
openblas-srpm-macros-2-19.el10.noarch
openldap-2.6.10-1.el10.aarch64
openssl-fips-provider-3.5.1-6.el10.aarch64
openssl-libs-3.5.1-6.el10.aarch64
p11-kit-0.26.1-1.el10.aarch64
p11-kit-trust-0.26.1-1.el10.aarch64
package-notes-srpm-macros-0.5-13.el10.noarch
pam-1.6.1-9.el10.aarch64
pam-libs-1.6.1-9.el10.aarch64
patch-2.7.6-26.el10.aarch64
pcre2-10.44-1.el10.3.aarch64
pcre2-syntax-10.44-1.el10.3.noarch
perl-srpm-macros-1-57.el10.noarch
pkgconf-2.1.0-3.el10.aarch64
pkgconf-m4-2.1.0-3.el10.noarch
pkgconf-pkg-config-2.1.0-3.el10.aarch64
popt-1.19-8.el10.aarch64
publicsuffix-list-dafsa-20240107-5.el10.noarch
pyproject-srpm-macros-1.18.5-1.el10.noarch
python-srpm-macros-3.12-11.el10.noarch
qt6-srpm-macros-6.10.1-1.el10.noarch
readline-8.2-11.el10.aarch64
redhat-rpm-config-295-1.el10.noarch
rpm-4.19.1.1-21.el10.aarch64
rpm-build-4.19.1.1-21.el10.aarch64
rpm-build-libs-4.19.1.1-21.el10.aarch64
rpm-libs-4.19.1.1-21.el10.aarch64
rpm-sequoia-1.9.0.3-1.el10.aarch64
rust-toolset-srpm-macros-1.92.0-1.el10.noarch
sed-4.9-3.el10.aarch64
setup-2.14.5-7.el10.noarch
shadow-utils-4.15.0-9.el10.aarch64
sqlite-libs-3.46.1-5.el10.aarch64
systemd-libs-257-21.el10.aarch64
tar-1.35-10.el10.aarch64
unzip-6.0-69.el10.aarch64
util-linux-2.40.2-13.el10.aarch64
util-linux-core-2.40.2-13.el10.aarch64
which-2.21-44.el10.aarch64
xz-5.6.2-4.el10.aarch64
xz-libs-5.6.2-4.el10.aarch64
zip-3.0-45.el10.aarch64
zlib-ng-compat-2.2.3-3.el10.aarch64
zstd-1.5.5-9.el10.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/bcftools-1.23-1.el10.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root/var/log/dnf.rpm.log
/var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root/var/log/dnf.librepo.log
/var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root/var/log/dnf.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-oqcscjcn/bcftools/bcftools.spec) Config(child) 0 minutes 28 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/bcftools-1.23-1.el10.src.rpm)  Config(centos-stream+epel-10-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769502044.615196/root.
INFO: reusing tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-bootstrap-1769502044.615196/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1.1-21.el10.aarch64
  rpm-sequoia-1.9.0.3-1.el10.aarch64
  python3-dnf-4.20.0-19.el10.noarch
  python3-dnf-plugins-core-4.7.0-10.el10.noarch
  yum-4.20.0-19.el10.noarch
Finish: chroot init
Start: build phase for bcftools-1.23-1.el10.src.rpm
Start: build setup for bcftools-1.23-1.el10.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/bcftools-1.23-1.el10.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  66 kB/s | 1.5 kB     00:00    
CentOS Stream 10 - BaseOS                        78 kB/s | 5.5 kB     00:00    
CentOS Stream 10 - AppStream                    126 kB/s | 5.5 kB     00:00    
CentOS Stream 10 - CRB                           99 kB/s | 4.4 kB     00:00    
CentOS Stream 10 - Extras packages               41 kB/s | 7.4 kB     00:00    
Extra Packages for Enterprise Linux 10 - aarch6 132 kB/s |  13 kB     00:00    
Dependencies resolved.
================================================================================
 Package                   Arch      Version                  Repository   Size
================================================================================
Installing:
 autoconf                  noarch    2.71-13.el10             appstream   736 k
 automake                  noarch    1.16.5-20.el10           appstream   702 k
 gcc                       aarch64   14.3.1-4.2.el10          appstream    35 M
 gsl-devel                 aarch64   2.7.1-11.el10_0          epel        610 k
 htslib-devel              aarch64   1.23-1.el10              copr_base   107 k
 htslib-tools              aarch64   1.23-1.el10              copr_base   740 k
 make                      aarch64   1:4.4.1-9.el10           baseos      585 k
 perl-ExtUtils-Embed       noarch    1.35-514.el10            appstream    18 k
 perl-File-Temp            noarch    1:0.231.100-512.el10     baseos       60 k
 perl-FindBin              noarch    1.54-514.el10            appstream    15 k
 perl-Getopt-Long          noarch    1:2.58-3.el10            baseos       65 k
 perl-interpreter          aarch64   4:5.40.2-514.el10        appstream    73 k
 zlib-ng-compat-devel      aarch64   2.2.3-3.el10             appstream    36 k
Installing dependencies:
 annobin-docs              noarch    13.02-2.el10             appstream    87 k
 annobin-plugin-gcc        aarch64   13.02-2.el10             appstream   997 k
 cmake-filesystem          aarch64   3.31.8-1.el10            appstream    21 k
 cpp                       aarch64   14.3.1-4.2.el10          appstream    11 M
 emacs-filesystem          noarch    1:29.4-12.el10           appstream    10 k
 expat                     aarch64   2.7.3-1.el10             baseos      114 k
 gcc-plugin-annobin        aarch64   14.3.1-4.2.el10          appstream    69 k
 glibc-devel               aarch64   2.39-99.el10             appstream   589 k
 groff-base                aarch64   1.23.0-10.el10           baseos      1.1 M
 gsl                       aarch64   2.7.1-11.el10_0          epel        1.0 M
 htslib                    aarch64   1.23-1.el10              copr_base   560 k
 kernel-headers            aarch64   6.12.0-191.el10          appstream   3.1 M
 libasan                   aarch64   14.3.1-4.2.el10          appstream   532 k
 libatomic                 aarch64   14.3.1-4.2.el10          baseos       58 k
 libmpc                    aarch64   1.3.1-7.el10             appstream    73 k
 libubsan                  aarch64   14.3.1-4.2.el10          appstream   238 k
 libxcrypt-devel           aarch64   4.4.36-10.el10           appstream    30 k
 m4                        aarch64   1.4.19-11.el10           appstream   301 k
 mpdecimal                 aarch64   2.5.1-12.el10            baseos       90 k
 ncurses                   aarch64   6.4-14.20240127.el10     baseos      421 k
 perl-AutoLoader           noarch    5.74-514.el10            appstream    22 k
 perl-AutoSplit            noarch    5.74-514.el10            appstream    22 k
 perl-B                    aarch64   1.89-514.el10            appstream   179 k
 perl-Benchmark            noarch    1.25-514.el10            appstream    27 k
 perl-Carp                 noarch    1.54-511.el10            baseos       30 k
 perl-Class-Struct         noarch    0.68-514.el10            appstream    23 k
 perl-Data-Dumper          aarch64   2.189-512.el10           baseos       56 k
 perl-Devel-PPPort         aarch64   3.72-512.el10            appstream   217 k
 perl-Digest               noarch    1.20-511.el10            baseos       26 k
 perl-Digest-MD5           aarch64   2.59-6.el10              baseos       37 k
 perl-DynaLoader           aarch64   1.56-514.el10            appstream    27 k
 perl-Encode               aarch64   4:3.21-511.el10          baseos      1.1 M
 perl-Errno                aarch64   1.38-514.el10            appstream    16 k
 perl-Exporter             noarch    5.78-511.el10            baseos       32 k
 perl-ExtUtils-Command     noarch    2:7.70-513.el10          appstream    15 k
 perl-ExtUtils-Constant    noarch    0.25-514.el10            appstream    44 k
 perl-ExtUtils-Install     noarch    2.22-511.el10            appstream    44 k
 perl-ExtUtils-MakeMaker   noarch    2:7.70-513.el10          appstream   293 k
 perl-ExtUtils-Manifest    noarch    1:1.75-511.el10          appstream    35 k
 perl-ExtUtils-ParseXS     noarch    1:3.51-512.el10          appstream   186 k
 perl-Fcntl                aarch64   1.18-514.el10            appstream    30 k
 perl-File-Basename        noarch    2.86-514.el10            appstream    18 k
 perl-File-Compare         noarch    1.100.800-514.el10       appstream    14 k
 perl-File-Copy            noarch    2.41-514.el10            appstream    21 k
 perl-File-Find            noarch    1.44-514.el10            appstream    26 k
 perl-File-Path            noarch    2.18-512.el10            appstream    35 k
 perl-File-stat            noarch    1.14-514.el10            appstream    18 k
 perl-FileHandle           noarch    2.05-514.el10            appstream    16 k
 perl-Getopt-Std           noarch    1.14-514.el10            appstream    16 k
 perl-HTTP-Tiny            noarch    0.088-512.el10           baseos       57 k
 perl-IO                   aarch64   1.55-514.el10            appstream    81 k
 perl-IO-Socket-IP         noarch    0.42-512.el10            baseos       43 k
 perl-IO-Socket-SSL        noarch    2.085-3.el10             baseos      227 k
 perl-IPC-Open3            noarch    1.22-514.el10            appstream    23 k
 perl-MIME-Base64          aarch64   3.16-511.el10            baseos       31 k
 perl-Mozilla-CA           noarch    20231213-5.el10          baseos       15 k
 perl-Net-SSLeay           aarch64   1.94-8.el10              appstream   381 k
 perl-POSIX                aarch64   2.20-514.el10            appstream    98 k
 perl-PathTools            aarch64   3.91-512.el10            baseos       85 k
 perl-Pod-Escapes          noarch    1:1.07-511.el10          baseos       21 k
 perl-Pod-Perldoc          noarch    3.28.01-512.el10         baseos       84 k
 perl-Pod-Simple           noarch    1:3.45-511.el10          baseos      218 k
 perl-Pod-Usage            noarch    4:2.03-511.el10          baseos       41 k
 perl-Scalar-List-Utils    aarch64   5:1.63-511.el10          baseos       73 k
 perl-SelectSaver          noarch    1.02-514.el10            appstream    12 k
 perl-Socket               aarch64   4:2.038-511.el10         baseos       56 k
 perl-Storable             aarch64   1:3.32-511.el10          baseos       98 k
 perl-Symbol               noarch    1.09-514.el10            appstream    15 k
 perl-Term-ANSIColor       noarch    5.01-512.el10            baseos       49 k
 perl-Term-Cap             noarch    1.18-511.el10            baseos       23 k
 perl-Test-Harness         noarch    1:3.48-512.el10          appstream   284 k
 perl-Text-ParseWords      noarch    3.31-511.el10            baseos       17 k
 perl-Text-Tabs+Wrap       noarch    2024.001-511.el10        baseos       23 k
 perl-Thread-Queue         noarch    3.14-511.el10            appstream    22 k
 perl-Time-Local           noarch    2:1.350-511.el10         baseos       35 k
 perl-URI                  noarch    5.27-3.el10              baseos      134 k
 perl-base                 noarch    2.27-514.el10            appstream    17 k
 perl-constant             noarch    1.33-512.el10            baseos       24 k
 perl-devel                aarch64   4:5.40.2-514.el10        appstream   768 k
 perl-if                   noarch    0.61.000-514.el10        appstream    15 k
 perl-lib                  aarch64   0.65-514.el10            appstream    16 k
 perl-libnet               noarch    3.15-512.el10            baseos      127 k
 perl-libs                 aarch64   4:5.40.2-514.el10        appstream   2.3 M
 perl-locale               noarch    1.12-514.el10            appstream    14 k
 perl-mro                  aarch64   1.29-514.el10            appstream    30 k
 perl-overload             noarch    1.37-514.el10            appstream    46 k
 perl-overloading          noarch    0.02-514.el10            appstream    14 k
 perl-parent               noarch    1:0.241-512.el10         baseos       16 k
 perl-podlators            noarch    1:5.01-511.el10          baseos      124 k
 perl-threads              aarch64   1:2.40-511.el10          appstream    58 k
 perl-threads-shared       aarch64   1.69-511.el10            appstream    45 k
 perl-vars                 noarch    1.05-514.el10            appstream    14 k
 perl-version              aarch64   8:0.99.32-4.el10         appstream    63 k
 python3                   aarch64   3.12.12-3.el10           baseos       28 k
 python3-libs              aarch64   3.12.12-3.el10           baseos      9.3 M
 python3-pip-wheel         noarch    23.3.2-7.el10            baseos      1.5 M
 python3-pyparsing         noarch    3.1.1-7.el10             baseos      269 k
 systemtap-sdt-devel       aarch64   5.4-3.el10               appstream    69 k
 systemtap-sdt-dtrace      aarch64   5.4-3.el10               appstream    70 k
 tzdata                    noarch    2025c-1.el10             baseos      904 k

Transaction Summary
================================================================================
Install  113 Packages

Total download size: 79 M
Installed size: 252 M
Downloading Packages:
(1/113): htslib-devel-1.23-1.el10.aarch64.rpm   6.3 MB/s | 107 kB     00:00    
(2/113): htslib-tools-1.23-1.el10.aarch64.rpm    33 MB/s | 740 kB     00:00    
(3/113): htslib-1.23-1.el10.aarch64.rpm          19 MB/s | 560 kB     00:00    
(4/113): expat-2.7.3-1.el10.aarch64.rpm         9.3 MB/s | 114 kB     00:00    
(5/113): groff-base-1.23.0-10.el10.aarch64.rpm   86 MB/s | 1.1 MB     00:00    
(6/113): libatomic-14.3.1-4.2.el10.aarch64.rpm  7.8 MB/s |  58 kB     00:00    
(7/113): make-4.4.1-9.el10.aarch64.rpm           53 MB/s | 585 kB     00:00    
(8/113): mpdecimal-2.5.1-12.el10.aarch64.rpm     19 MB/s |  90 kB     00:00    
(9/113): ncurses-6.4-14.20240127.el10.aarch64.r  69 MB/s | 421 kB     00:00    
(10/113): perl-Carp-1.54-511.el10.noarch.rpm     11 MB/s |  30 kB     00:00    
(11/113): perl-Data-Dumper-2.189-512.el10.aarch  22 MB/s |  56 kB     00:00    
(12/113): perl-Digest-1.20-511.el10.noarch.rpm   12 MB/s |  26 kB     00:00    
(13/113): perl-Digest-MD5-2.59-6.el10.aarch64.r  15 MB/s |  37 kB     00:00    
(14/113): perl-Exporter-5.78-511.el10.noarch.rp  14 MB/s |  32 kB     00:00    
(15/113): perl-File-Temp-0.231.100-512.el10.noa  25 MB/s |  60 kB     00:00    
(16/113): perl-Getopt-Long-2.58-3.el10.noarch.r  18 MB/s |  65 kB     00:00    
(17/113): perl-HTTP-Tiny-0.088-512.el10.noarch.  21 MB/s |  57 kB     00:00    
(18/113): perl-IO-Socket-IP-0.42-512.el10.noarc  15 MB/s |  43 kB     00:00    
(19/113): perl-IO-Socket-SSL-2.085-3.el10.noarc  51 MB/s | 227 kB     00:00    
(20/113): perl-Encode-3.21-511.el10.aarch64.rpm  76 MB/s | 1.1 MB     00:00    
(21/113): perl-MIME-Base64-3.16-511.el10.aarch6 8.4 MB/s |  31 kB     00:00    
(22/113): perl-Mozilla-CA-20231213-5.el10.noarc 6.4 MB/s |  15 kB     00:00    
(23/113): perl-Pod-Escapes-1.07-511.el10.noarch 6.3 MB/s |  21 kB     00:00    
(24/113): perl-PathTools-3.91-512.el10.aarch64.  19 MB/s |  85 kB     00:00    
(25/113): perl-Pod-Perldoc-3.28.01-512.el10.noa  21 MB/s |  84 kB     00:00    
(26/113): perl-Pod-Usage-2.03-511.el10.noarch.r  17 MB/s |  41 kB     00:00    
(27/113): perl-Pod-Simple-3.45-511.el10.noarch.  49 MB/s | 218 kB     00:00    
(28/113): perl-Scalar-List-Utils-1.63-511.el10.  17 MB/s |  73 kB     00:00    
(29/113): perl-Socket-2.038-511.el10.aarch64.rp  23 MB/s |  56 kB     00:00    
(30/113): perl-Term-ANSIColor-5.01-512.el10.noa  19 MB/s |  49 kB     00:00    
(31/113): perl-Storable-3.32-511.el10.aarch64.r  23 MB/s |  98 kB     00:00    
(32/113): perl-Term-Cap-1.18-511.el10.noarch.rp 8.2 MB/s |  23 kB     00:00    
(33/113): perl-Text-ParseWords-3.31-511.el10.no 6.8 MB/s |  17 kB     00:00    
(34/113): perl-Text-Tabs+Wrap-2024.001-511.el10 8.9 MB/s |  23 kB     00:00    
(35/113): perl-Time-Local-1.350-511.el10.noarch  12 MB/s |  35 kB     00:00    
(36/113): perl-constant-1.33-512.el10.noarch.rp 9.8 MB/s |  24 kB     00:00    
(37/113): perl-URI-5.27-3.el10.noarch.rpm        33 MB/s | 134 kB     00:00    
(38/113): perl-libnet-3.15-512.el10.noarch.rpm   29 MB/s | 127 kB     00:00    
(39/113): perl-parent-0.241-512.el10.noarch.rpm 6.1 MB/s |  16 kB     00:00    
(40/113): perl-podlators-5.01-511.el10.noarch.r  35 MB/s | 124 kB     00:00    
(41/113): python3-3.12.12-3.el10.aarch64.rpm    7.8 MB/s |  28 kB     00:00    
(42/113): python3-pyparsing-3.1.1-7.el10.noarch  10 MB/s | 269 kB     00:00    
(43/113): python3-libs-3.12.12-3.el10.aarch64.r 242 MB/s | 9.3 MB     00:00    
(44/113): python3-pip-wheel-23.3.2-7.el10.noarc  37 MB/s | 1.5 MB     00:00    
(45/113): tzdata-2025c-1.el10.noarch.rpm         54 MB/s | 904 kB     00:00    
(46/113): annobin-docs-13.02-2.el10.noarch.rpm   12 MB/s |  87 kB     00:00    
(47/113): annobin-plugin-gcc-13.02-2.el10.aarch 121 MB/s | 997 kB     00:00    
(48/113): autoconf-2.71-13.el10.noarch.rpm       94 MB/s | 736 kB     00:00    
(49/113): automake-1.16.5-20.el10.noarch.rpm     71 MB/s | 702 kB     00:00    
(50/113): cmake-filesystem-3.31.8-1.el10.aarch6 3.8 MB/s |  21 kB     00:00    
(51/113): emacs-filesystem-29.4-12.el10.noarch. 2.6 MB/s |  10 kB     00:00    
(52/113): gcc-plugin-annobin-14.3.1-4.2.el10.aa 5.0 MB/s |  69 kB     00:00    
(53/113): glibc-devel-2.39-99.el10.aarch64.rpm   16 MB/s | 589 kB     00:00    
(54/113): cpp-14.3.1-4.2.el10.aarch64.rpm       160 MB/s |  11 MB     00:00    
(55/113): kernel-headers-6.12.0-191.el10.aarch6  59 MB/s | 3.1 MB     00:00    
(56/113): libasan-14.3.1-4.2.el10.aarch64.rpm    11 MB/s | 532 kB     00:00    
(57/113): gcc-14.3.1-4.2.el10.aarch64.rpm       202 MB/s |  35 MB     00:00    
(58/113): libmpc-1.3.1-7.el10.aarch64.rpm       1.1 MB/s |  73 kB     00:00    
(59/113): libubsan-14.3.1-4.2.el10.aarch64.rpm  4.2 MB/s | 238 kB     00:00    
(60/113): libxcrypt-devel-4.4.36-10.el10.aarch6  11 MB/s |  30 kB     00:00    
(61/113): perl-AutoLoader-5.74-514.el10.noarch. 4.0 MB/s |  22 kB     00:00    
(62/113): m4-1.4.19-11.el10.aarch64.rpm          39 MB/s | 301 kB     00:00    
(63/113): perl-AutoSplit-5.74-514.el10.noarch.r 3.4 MB/s |  22 kB     00:00    
(64/113): perl-Benchmark-1.25-514.el10.noarch.r 3.7 MB/s |  27 kB     00:00    
(65/113): perl-Class-Struct-0.68-514.el10.noarc 3.5 MB/s |  23 kB     00:00    
(66/113): perl-B-1.89-514.el10.aarch64.rpm       18 MB/s | 179 kB     00:00    
(67/113): perl-DynaLoader-1.56-514.el10.aarch64 3.6 MB/s |  27 kB     00:00    
(68/113): perl-Errno-1.38-514.el10.aarch64.rpm  2.2 MB/s |  16 kB     00:00    
(69/113): perl-Devel-PPPort-3.72-512.el10.aarch  15 MB/s | 217 kB     00:00    
(70/113): perl-ExtUtils-Command-7.70-513.el10.n 1.2 MB/s |  15 kB     00:00    
(71/113): perl-ExtUtils-Constant-0.25-514.el10. 2.4 MB/s |  44 kB     00:00    
(72/113): perl-ExtUtils-Install-2.22-511.el10.n 3.7 MB/s |  44 kB     00:00    
(73/113): perl-ExtUtils-Embed-1.35-514.el10.noa 997 kB/s |  18 kB     00:00    
(74/113): perl-ExtUtils-MakeMaker-7.70-513.el10  36 MB/s | 293 kB     00:00    
(75/113): perl-ExtUtils-Manifest-1.75-511.el10.  10 MB/s |  35 kB     00:00    
(76/113): perl-Fcntl-1.18-514.el10.aarch64.rpm   14 MB/s |  30 kB     00:00    
(77/113): perl-ExtUtils-ParseXS-3.51-512.el10.n  39 MB/s | 186 kB     00:00    
(78/113): perl-File-Basename-2.86-514.el10.noar 7.8 MB/s |  18 kB     00:00    
(79/113): perl-File-Compare-1.100.800-514.el10. 5.3 MB/s |  14 kB     00:00    
(80/113): perl-File-Copy-2.41-514.el10.noarch.r 8.5 MB/s |  21 kB     00:00    
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(98/113): perl-interpreter-5.40.2-514.el10.aarc  13 MB/s |  73 kB     00:00    
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(100/113): perl-locale-1.12-514.el10.noarch.rpm 5.4 MB/s |  14 kB     00:00    
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(102/113): perl-overload-1.37-514.el10.noarch.r  10 MB/s |  46 kB     00:00    
(103/113): perl-overloading-0.02-514.el10.noarc 3.0 MB/s |  14 kB     00:00    
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(105/113): perl-libs-5.40.2-514.el10.aarch64.rp 156 MB/s | 2.3 MB     00:00    
(106/113): perl-threads-shared-1.69-511.el10.aa 6.2 MB/s |  45 kB     00:00    
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(108/113): perl-version-0.99.32-4.el10.aarch64.  21 MB/s |  63 kB     00:00    
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(111/113): zlib-ng-compat-devel-2.2.3-3.el10.aa  13 MB/s |  36 kB     00:00    
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(113/113): gsl-devel-2.7.1-11.el10_0.aarch64.rp 3.5 MB/s | 610 kB     00:00    
--------------------------------------------------------------------------------
Total                                            74 MB/s |  79 MB     00:01     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
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  Installing       : mpdecimal-2.5.1-12.el10.aarch64                     17/113 
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  Installing       : perl-Pod-Perldoc-3.28.01-512.el10.noarch            53/113 
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  Installing       : python3-3.12.12-3.el10.aarch64                      98/113 
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  Installing       : perl-ExtUtils-MakeMaker-2:7.70-513.el10.noarch     105/113 
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  Installing       : perl-FindBin-1.54-514.el10.noarch                  108/113 
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  Installing       : gcc-plugin-annobin-14.3.1-4.2.el10.aarch64         110/113 
  Running scriptlet: gcc-plugin-annobin-14.3.1-4.2.el10.aarch64         110/113 
  Installing       : zlib-ng-compat-devel-2.2.3-3.el10.aarch64          111/113 
  Installing       : htslib-devel-1.23-1.el10.aarch64                   112/113 
  Installing       : htslib-tools-1.23-1.el10.aarch64                   113/113 
  Running scriptlet: htslib-tools-1.23-1.el10.aarch64                   113/113 

Installed:
  annobin-docs-13.02-2.el10.noarch                                              
  annobin-plugin-gcc-13.02-2.el10.aarch64                                       
  autoconf-2.71-13.el10.noarch                                                  
  automake-1.16.5-20.el10.noarch                                                
  cmake-filesystem-3.31.8-1.el10.aarch64                                        
  cpp-14.3.1-4.2.el10.aarch64                                                   
  emacs-filesystem-1:29.4-12.el10.noarch                                        
  expat-2.7.3-1.el10.aarch64                                                    
  gcc-14.3.1-4.2.el10.aarch64                                                   
  gcc-plugin-annobin-14.3.1-4.2.el10.aarch64                                    
  glibc-devel-2.39-99.el10.aarch64                                              
  groff-base-1.23.0-10.el10.aarch64                                             
  gsl-2.7.1-11.el10_0.aarch64                                                   
  gsl-devel-2.7.1-11.el10_0.aarch64                                             
  htslib-1.23-1.el10.aarch64                                                    
  htslib-devel-1.23-1.el10.aarch64                                              
  htslib-tools-1.23-1.el10.aarch64                                              
  kernel-headers-6.12.0-191.el10.aarch64                                        
  libasan-14.3.1-4.2.el10.aarch64                                               
  libatomic-14.3.1-4.2.el10.aarch64                                             
  libmpc-1.3.1-7.el10.aarch64                                                   
  libubsan-14.3.1-4.2.el10.aarch64                                              
  libxcrypt-devel-4.4.36-10.el10.aarch64                                        
  m4-1.4.19-11.el10.aarch64                                                     
  make-1:4.4.1-9.el10.aarch64                                                   
  mpdecimal-2.5.1-12.el10.aarch64                                               
  ncurses-6.4-14.20240127.el10.aarch64                                          
  perl-AutoLoader-5.74-514.el10.noarch                                          
  perl-AutoSplit-5.74-514.el10.noarch                                           
  perl-B-1.89-514.el10.aarch64                                                  
  perl-Benchmark-1.25-514.el10.noarch                                           
  perl-Carp-1.54-511.el10.noarch                                                
  perl-Class-Struct-0.68-514.el10.noarch                                        
  perl-Data-Dumper-2.189-512.el10.aarch64                                       
  perl-Devel-PPPort-3.72-512.el10.aarch64                                       
  perl-Digest-1.20-511.el10.noarch                                              
  perl-Digest-MD5-2.59-6.el10.aarch64                                           
  perl-DynaLoader-1.56-514.el10.aarch64                                         
  perl-Encode-4:3.21-511.el10.aarch64                                           
  perl-Errno-1.38-514.el10.aarch64                                              
  perl-Exporter-5.78-511.el10.noarch                                            
  perl-ExtUtils-Command-2:7.70-513.el10.noarch                                  
  perl-ExtUtils-Constant-0.25-514.el10.noarch                                   
  perl-ExtUtils-Embed-1.35-514.el10.noarch                                      
  perl-ExtUtils-Install-2.22-511.el10.noarch                                    
  perl-ExtUtils-MakeMaker-2:7.70-513.el10.noarch                                
  perl-ExtUtils-Manifest-1:1.75-511.el10.noarch                                 
  perl-ExtUtils-ParseXS-1:3.51-512.el10.noarch                                  
  perl-Fcntl-1.18-514.el10.aarch64                                              
  perl-File-Basename-2.86-514.el10.noarch                                       
  perl-File-Compare-1.100.800-514.el10.noarch                                   
  perl-File-Copy-2.41-514.el10.noarch                                           
  perl-File-Find-1.44-514.el10.noarch                                           
  perl-File-Path-2.18-512.el10.noarch                                           
  perl-File-Temp-1:0.231.100-512.el10.noarch                                    
  perl-File-stat-1.14-514.el10.noarch                                           
  perl-FileHandle-2.05-514.el10.noarch                                          
  perl-FindBin-1.54-514.el10.noarch                                             
  perl-Getopt-Long-1:2.58-3.el10.noarch                                         
  perl-Getopt-Std-1.14-514.el10.noarch                                          
  perl-HTTP-Tiny-0.088-512.el10.noarch                                          
  perl-IO-1.55-514.el10.aarch64                                                 
  perl-IO-Socket-IP-0.42-512.el10.noarch                                        
  perl-IO-Socket-SSL-2.085-3.el10.noarch                                        
  perl-IPC-Open3-1.22-514.el10.noarch                                           
  perl-MIME-Base64-3.16-511.el10.aarch64                                        
  perl-Mozilla-CA-20231213-5.el10.noarch                                        
  perl-Net-SSLeay-1.94-8.el10.aarch64                                           
  perl-POSIX-2.20-514.el10.aarch64                                              
  perl-PathTools-3.91-512.el10.aarch64                                          
  perl-Pod-Escapes-1:1.07-511.el10.noarch                                       
  perl-Pod-Perldoc-3.28.01-512.el10.noarch                                      
  perl-Pod-Simple-1:3.45-511.el10.noarch                                        
  perl-Pod-Usage-4:2.03-511.el10.noarch                                         
  perl-Scalar-List-Utils-5:1.63-511.el10.aarch64                                
  perl-SelectSaver-1.02-514.el10.noarch                                         
  perl-Socket-4:2.038-511.el10.aarch64                                          
  perl-Storable-1:3.32-511.el10.aarch64                                         
  perl-Symbol-1.09-514.el10.noarch                                              
  perl-Term-ANSIColor-5.01-512.el10.noarch                                      
  perl-Term-Cap-1.18-511.el10.noarch                                            
  perl-Test-Harness-1:3.48-512.el10.noarch                                      
  perl-Text-ParseWords-3.31-511.el10.noarch                                     
  perl-Text-Tabs+Wrap-2024.001-511.el10.noarch                                  
  perl-Thread-Queue-3.14-511.el10.noarch                                        
  perl-Time-Local-2:1.350-511.el10.noarch                                       
  perl-URI-5.27-3.el10.noarch                                                   
  perl-base-2.27-514.el10.noarch                                                
  perl-constant-1.33-512.el10.noarch                                            
  perl-devel-4:5.40.2-514.el10.aarch64                                          
  perl-if-0.61.000-514.el10.noarch                                              
  perl-interpreter-4:5.40.2-514.el10.aarch64                                    
  perl-lib-0.65-514.el10.aarch64                                                
  perl-libnet-3.15-512.el10.noarch                                              
  perl-libs-4:5.40.2-514.el10.aarch64                                           
  perl-locale-1.12-514.el10.noarch                                              
  perl-mro-1.29-514.el10.aarch64                                                
  perl-overload-1.37-514.el10.noarch                                            
  perl-overloading-0.02-514.el10.noarch                                         
  perl-parent-1:0.241-512.el10.noarch                                           
  perl-podlators-1:5.01-511.el10.noarch                                         
  perl-threads-1:2.40-511.el10.aarch64                                          
  perl-threads-shared-1.69-511.el10.aarch64                                     
  perl-vars-1.05-514.el10.noarch                                                
  perl-version-8:0.99.32-4.el10.aarch64                                         
  python3-3.12.12-3.el10.aarch64                                                
  python3-libs-3.12.12-3.el10.aarch64                                           
  python3-pip-wheel-23.3.2-7.el10.noarch                                        
  python3-pyparsing-3.1.1-7.el10.noarch                                         
  systemtap-sdt-devel-5.4-3.el10.aarch64                                        
  systemtap-sdt-dtrace-5.4-3.el10.aarch64                                       
  tzdata-2025c-1.el10.noarch                                                    
  zlib-ng-compat-devel-2.2.3-3.el10.aarch64                                     

Complete!
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/bcftools-1.23-1.el10.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  24 kB/s | 1.5 kB     00:00    
CentOS Stream 10 - BaseOS                       117 kB/s | 5.5 kB     00:00    
CentOS Stream 10 - AppStream                    106 kB/s | 5.5 kB     00:00    
CentOS Stream 10 - CRB                           63 kB/s | 4.4 kB     00:00    
CentOS Stream 10 - Extras packages              144 kB/s | 7.4 kB     00:00    
Extra Packages for Enterprise Linux 10 - aarch6  48 kB/s |  13 kB     00:00    
Package autoconf-2.71-13.el10.noarch is already installed.
Package automake-1.16.5-20.el10.noarch is already installed.
Package gcc-14.3.1-4.2.el10.aarch64 is already installed.
Package gsl-devel-2.7.1-11.el10_0.aarch64 is already installed.
Package htslib-devel-1.23-1.el10.aarch64 is already installed.
Package htslib-tools-1.23-1.el10.aarch64 is already installed.
Package make-1:4.4.1-9.el10.aarch64 is already installed.
Package perl-ExtUtils-Embed-1.35-514.el10.noarch is already installed.
Package perl-File-Temp-1:0.231.100-512.el10.noarch is already installed.
Package perl-FindBin-1.54-514.el10.noarch is already installed.
Package perl-Getopt-Long-1:2.58-3.el10.noarch is already installed.
Package perl-interpreter-4:5.40.2-514.el10.aarch64 is already installed.
Package zlib-ng-compat-devel-2.2.3-3.el10.aarch64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!
Finish: build setup for bcftools-1.23-1.el10.src.rpm
Start: rpmbuild bcftools-1.23-1.el10.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.N2QLRT
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bcftools-1.23
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bcftools-1.23.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bcftools-1.23
+ rm -rf /builddir/build/BUILD/bcftools-1.23-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.23-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (bcftools-1.23-perl-fix-stray-errors-ldflags.patch):'
Patch #0 (bcftools-1.23-perl-fix-stray-errors-ldflags.patch):
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0
patching file configure.ac
+ sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats
+ sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.rroHwc
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bcftools-1.23
+ autoreconf -fiv
autoreconf: export WARNINGS=
autoreconf: Entering directory '.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force 
autoreconf: configure.ac: tracing
autoreconf: configure.ac: subdirectory $HTSDIR not present
autoreconf: configure.ac: not using Libtool
autoreconf: configure.ac: not using Intltool
autoreconf: configure.ac: not using Gtkdoc
autoreconf: running: /usr/bin/autoconf --force
configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:94: the top level
autoreconf: running: /usr/bin/autoheader --force
autoreconf: configure.ac: not using Automake
autoreconf: Leaving directory '.'
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.23/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./htslib-1.23/config.guess
++ basename ./htslib-1.23/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./htslib-1.23/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './htslib-1.23/config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./htslib-1.23/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./htslib-1.23/config.sub
++ basename ./htslib-1.23/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection  ' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)'
checking for aarch64-redhat-linux-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking shared library type... plain .so
checking for library containing dlopen... none required
checking if the compiler accepts -rdynamic... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for gsl/gsl_version.h... yes
checking for library containing cblas_dgemm... -lgslcblas
checking for gsl_multifit_gradient in -lgsl... yes
configure: removing -specs=...redhat-hardened... from Perl options
checking for library containing Perl_call_pv... -lperl
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
configure: License has been changed to GPL.

Linking against the GNU scientific library requires that the resulting
binary is licensed using the GNU General Public License.  In particular,
this means you will have to follow the terms of this license in order
to distribute binary copies.  For more information see the INSTALL file.

Text of the GNU General Public License can be found in the LICENSE file,
or at http://www.gnu.org/copyleft/gpl.html

Information on the GNU Scientific Library, including the rationale for
its choice of license can be found at https://www.gnu.org/software/gsl/

+ /usr/bin/make -O -j4 V=1 VERBOSE=1
echo '#define BCFTOOLS_VERSION "1.23"' > version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfindex.o vcfindex.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfisec.o vcfisec.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfquery.o vcfquery.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcffilter.o vcffilter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfstats.o vcfstats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfsom.o vcfsom.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfgtcheck.o vcfgtcheck.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfview.o vcfview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfmerge.o vcfmerge.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfnorm.o vcfnorm.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfroh.o vcfroh.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfconcat.o vcfconcat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcmp.o vcmp.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o gvcf.o gvcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfcall.o vcfcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o mcall.o mcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfannotate.o vcfannotate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o reheader.o reheader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o tsv2vcf.o tsv2vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfhead.o vcfhead.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o HMM.o HMM.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfcnv.o vcfcnv.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfconvert.o vcfconvert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o ploidy.o ploidy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o bin.o bin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o hclust.o hclust.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o version.o version.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o convert.o convert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o consensus.o consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o smpl_ilist.o smpl_ilist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfbuf.o vcfbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o mpileup.o mpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o bam2bcf.o bam2bcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o bam2bcf_iaux.o bam2bcf_iaux.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o read_consensus.o read_consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o bam2bcf_edlib.o bam2bcf_edlib.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o bam_sample.o bam_sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o cols.o cols.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o dist.o dist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o extsort.o extsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o vcfsort.o vcfsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o ccall.o ccall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o csq.o csq.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o em.o em.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o kmin.o kmin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o str_finder.o str_finder.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o abuf.o abuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o prob1.o prob1.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o edlib.o edlib.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o mpileup2/mpileup.o mpileup2/mpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o peakfit.o peakfit.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o polysomy.o polysomy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o test/test-rbuf.o test/test-rbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o gff.o gff.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.   -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -c -o test/test-regidx.o test/test-regidx.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/GTsubset.so version.c plugins/GTsubset.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/add-variantkey.so version.c plugins/add-variantkey.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/GTisec.so version.c plugins/GTisec.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/allele-length.so version.c plugins/allele-length.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/af-dist.so bin.c version.c plugins/af-dist.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/check-ploidy.so version.c plugins/check-ploidy.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/check-sparsity.so version.c plugins/check-sparsity.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/counts.so version.c plugins/counts.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/contrast.so version.c plugins/contrast.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/dosage.so version.c plugins/dosage.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/fixref.so version.c plugins/fixref.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/frameshifts.so version.c plugins/frameshifts.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/fill-tags.so version.c plugins/fill-tags.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/impute-info.so version.c plugins/impute-info.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/gvcfz.so version.c plugins/gvcfz.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/indel-stats.so version.c plugins/indel-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/missing2ref.so version.c plugins/missing2ref.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/mendelian2.so version.c plugins/mendelian2.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/parental-origin.so version.c plugins/parental-origin.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/prune.so version.c plugins/prune.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/scatter.so version.c plugins/scatter.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/setGT.so version.c plugins/setGT.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/smpl-stats.so version.c plugins/smpl-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/tag2tag.so version.c plugins/tag2tag.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/split.so version.c plugins/split.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/split-vep.so version.c plugins/split-vep.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/variant-distance.so version.c plugins/variant-distance.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/trio-stats.so version.c plugins/trio-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c 
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.   -DUSE_GPL -c -o main.o main.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c 
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o test/test-rbuf test/test-rbuf.o -lz  
gcc  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/vrfs.so version.c plugins/vrfs.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o plugins/vcf2table.so version.c plugins/vcf2table.c 
gcc -rdynamic  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o mpileup2/mpileup.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz   -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.r9H5FP
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64
++ dirname /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bcftools-1.23
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/bin /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/libexec/bcftools
/usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/bin
/usr/bin/install -p misc/color-chrs.pl misc/gff2gff misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/roh-viz misc/run-roh.pl misc/vcfutils.pl misc/vrfs-variances /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/bin
/usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/man/man1
/usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/libexec/bcftools
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.el10 --unique-debug-suffix -1.23-1.el10.aarch64 --unique-debug-src-base bcftools-1.23-1.el10.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.23
find-debuginfo: starting
Extracting debug info from 42 files
DWARF-compressing 42 files
sepdebugcrcfix: Updated 42 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/bcftools-1.23-1.el10.aarch64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/vrfs-variances from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/roh-viz from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/gff2gff from /usr/bin/env perl to #!/usr/bin/perl
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.j6cMFF
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection   -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bcftools-1.23
+ ldd bcftools
+ grep -E '/lib(64)?/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x0000ffff93a60000)
+ make test
./test/test-rbuf
Inserted 1-9 starting at offset 5:
  5  6  7  8  9  0  1  2  3
  1  2  3  4  5  6  7  8  9
4th is 4
Deleting 1-2:
  7  8  9  0  1  2  3
  3  4  5  6  7  8  9
Prepending 0-8:
  8  9  0  1  2  3  4  5  6  7
  8  7  6  5  4  3  2  1  0  3
Expanding:
  8  9 10 11 12 13 14 15 16 17
  8  7  6  5  4  3  2  1  0  3
./test/test-regidx
REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-}
./test/test.pl: module IO::Pty not found; skipping usage tests
test_usage:
	bcftools
test_tabix:
	tabix /tmp/BaL6TwCRH7/merge.a.vcf.gz 2:3199812-3199812
.. ok

test_tabix:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/merge.a.bcf 2:3199812-3199812
.. ok

test_tabix:
	tabix /tmp/BaL6TwCRH7/merge.a.vcf.gz 1:3000151-3000151
.. ok

test_tabix:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/merge.a.bcf 1:3000151-3000151
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.vcf.gz chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.bcf chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.bcf chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.vcf.gz chr20
.. ok

test_index:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/BaL6TwCRH7/large_chrom_csi_limit.bcf chr20
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/BaL6TwCRH7/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/BaL6TwCRH7/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/BaL6TwCRH7/idx.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/idx.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/idx.vcf.gz.csi
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/idx.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/idx.bcf.csi
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/BaL6TwCRH7/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/BaL6TwCRH7/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/BaL6TwCRH7/empty.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/empty.vcf.gz
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/empty.vcf.gz.csi
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/empty.bcf
.. ok

test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/BaL6TwCRH7/empty.bcf.csi
.. ok

test_vcf_check:
	/builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/BaL6TwCRH7/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok

test_vcf_check:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok

test_vcf_check_merge:
	/builddir/build/BUILD/bcftools-1.23/misc/plot-vcfstats -m /tmp/BaL6TwCRH7/check.1.chk /tmp/BaL6TwCRH7/check.2.chk /tmp/BaL6TwCRH7/check.3.chk /tmp/BaL6TwCRH7/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.23/bcftools stats -s -  /tmp/BaL6TwCRH7/stats.a.vcf.gz /tmp/BaL6TwCRH7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.23/bcftools stats -s B  /tmp/BaL6TwCRH7/stats.a.vcf.gz /tmp/BaL6TwCRH7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.23/bcftools stats -s -  /tmp/BaL6TwCRH7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.23/bcftools stats -s - -i 'type="snp"'  /tmp/BaL6TwCRH7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.23/bcftools stats -s -  /tmp/BaL6TwCRH7/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -w 2 --no-version /tmp/BaL6TwCRH7/isec.match-id.1.1.vcf.gz /tmp/BaL6TwCRH7/isec.match-id.1.2.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -w 2 -c id --no-version /tmp/BaL6TwCRH7/isec.match-id.1.1.vcf.gz /tmp/BaL6TwCRH7/isec.match-id.1.2.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 /tmp/BaL6TwCRH7/isec.a.vcf.gz /tmp/BaL6TwCRH7/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/BaL6TwCRH7/isec.a.vcf.gz /tmp/BaL6TwCRH7/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -c both /tmp/BaL6TwCRH7/isec.a.vcf.gz /tmp/BaL6TwCRH7/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -c any /tmp/BaL6TwCRH7/isec.a.vcf.gz /tmp/BaL6TwCRH7/isec.b.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -C -c any /tmp/BaL6TwCRH7/isec.a.vcf.gz /tmp/BaL6TwCRH7/isec.b.vcf.gz
.. ok

test_vcf_isec2:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec --no-version   -T /tmp/BaL6TwCRH7/isec.tab.gz /tmp/BaL6TwCRH7/isec.a.vcf.gz
.. ok

test_vcf_isec2:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -Ob  -T /tmp/BaL6TwCRH7/isec.tab.gz /tmp/BaL6TwCRH7/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/BaL6TwCRH7/isec-miss.1.1.vcf.gz /tmp/BaL6TwCRH7/isec-miss.1.2.vcf.gz /tmp/BaL6TwCRH7/isec-miss.1.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -R /builddir/build/BUILD/bcftools-1.23/test/isec-miss.1.regs.txt -n +1 /tmp/BaL6TwCRH7/isec-miss.1.1.vcf.gz /tmp/BaL6TwCRH7/isec-miss.1.2.vcf.gz /tmp/BaL6TwCRH7/isec-miss.1.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/BaL6TwCRH7/isec-miss.2.1.vcf.gz /tmp/BaL6TwCRH7/isec-miss.2.2.vcf.gz /tmp/BaL6TwCRH7/isec-miss.2.3.vcf.gz
.. ok

test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.23/bcftools isec -R /builddir/build/BUILD/bcftools-1.23/test/isec-miss.1.regs.txt -n +1 /tmp/BaL6TwCRH7/isec-miss.2.1.vcf.gz /tmp/BaL6TwCRH7/isec-miss.2.2.vcf.gz /tmp/BaL6TwCRH7/isec-miss.2.3.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.broken-gvcf.a.vcf.gz /tmp/BaL6TwCRH7/merge.broken-gvcf.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.broken-gvcf.a.vcf.gz /tmp/BaL6TwCRH7/merge.broken-gvcf.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.broken-gvcf.a.bcf /tmp/BaL6TwCRH7/merge.broken-gvcf.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.broken-gvcf.a.bcf /tmp/BaL6TwCRH7/merge.broken-gvcf.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.symbolic.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.symbolic.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.symbolic.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.symbolic.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.symbolic.1.a.bcf /tmp/BaL6TwCRH7/merge.symbolic.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.symbolic.1.a.bcf /tmp/BaL6TwCRH7/merge.symbolic.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/BaL6TwCRH7/merge.multiallelics.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.multiallelics.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/BaL6TwCRH7/merge.multiallelics.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.multiallelics.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/BaL6TwCRH7/merge.multiallelics.1.a.bcf /tmp/BaL6TwCRH7/merge.multiallelics.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/BaL6TwCRH7/merge.multiallelics.1.a.bcf /tmp/BaL6TwCRH7/merge.multiallelics.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/BaL6TwCRH7/merge.multiallelics.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.multiallelics.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/BaL6TwCRH7/merge.multiallelics.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.multiallelics.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/BaL6TwCRH7/merge.multiallelics.1.a.bcf /tmp/BaL6TwCRH7/merge.multiallelics.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/BaL6TwCRH7/merge.multiallelics.1.a.bcf /tmp/BaL6TwCRH7/merge.multiallelics.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/BaL6TwCRH7/merge.12.a.vcf.gz /tmp/BaL6TwCRH7/merge.12.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/BaL6TwCRH7/merge.12.a.vcf.gz /tmp/BaL6TwCRH7/merge.12.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge none /tmp/BaL6TwCRH7/merge.12.a.bcf /tmp/BaL6TwCRH7/merge.12.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/BaL6TwCRH7/merge.12.a.bcf /tmp/BaL6TwCRH7/merge.12.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/BaL6TwCRH7/merge.12.a.vcf.gz /tmp/BaL6TwCRH7/merge.12.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/BaL6TwCRH7/merge.12.a.vcf.gz /tmp/BaL6TwCRH7/merge.12.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --merge both /tmp/BaL6TwCRH7/merge.12.a.bcf /tmp/BaL6TwCRH7/merge.12.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/BaL6TwCRH7/merge.12.a.bcf /tmp/BaL6TwCRH7/merge.12.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.phased.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.phased.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.phased.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.phased.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.phased.1.a.bcf /tmp/BaL6TwCRH7/merge.phased.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.phased.1.a.bcf /tmp/BaL6TwCRH7/merge.phased.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.11.a.vcf.gz /tmp/BaL6TwCRH7/merge.11.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.11.a.vcf.gz /tmp/BaL6TwCRH7/merge.11.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.11.a.bcf /tmp/BaL6TwCRH7/merge.11.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.11.a.bcf /tmp/BaL6TwCRH7/merge.11.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AF:join /tmp/BaL6TwCRH7/merge.join.a.vcf.gz /tmp/BaL6TwCRH7/merge.join.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AF:join /tmp/BaL6TwCRH7/merge.join.a.vcf.gz /tmp/BaL6TwCRH7/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AF:join /tmp/BaL6TwCRH7/merge.join.a.bcf /tmp/BaL6TwCRH7/merge.join.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AF:join /tmp/BaL6TwCRH7/merge.join.a.bcf /tmp/BaL6TwCRH7/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-single /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-single /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-single /tmp/BaL6TwCRH7/merge.LPL.a.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-single /tmp/BaL6TwCRH7/merge.LPL.a.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 1 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 1 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 2 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 2 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 3 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 3 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 4 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 4 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 5 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/BaL6TwCRH7/merge.LPL.a.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.b.vcf.gz /tmp/BaL6TwCRH7/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -L 5 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/BaL6TwCRH7/merge.LPL.a.bcf /tmp/BaL6TwCRH7/merge.LPL.b.bcf /tmp/BaL6TwCRH7/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/BaL6TwCRH7/merge.a.vcf.gz /tmp/BaL6TwCRH7/merge.b.vcf.gz /tmp/BaL6TwCRH7/merge.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/BaL6TwCRH7/merge.a.vcf.gz /tmp/BaL6TwCRH7/merge.b.vcf.gz /tmp/BaL6TwCRH7/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/BaL6TwCRH7/merge.a.bcf /tmp/BaL6TwCRH7/merge.b.bcf /tmp/BaL6TwCRH7/merge.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/BaL6TwCRH7/merge.a.bcf /tmp/BaL6TwCRH7/merge.b.bcf /tmp/BaL6TwCRH7/merge.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -Fx /tmp/BaL6TwCRH7/merge.a.vcf.gz /tmp/BaL6TwCRH7/merge.b.vcf.gz /tmp/BaL6TwCRH7/merge.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -Fx /tmp/BaL6TwCRH7/merge.a.vcf.gz /tmp/BaL6TwCRH7/merge.b.vcf.gz /tmp/BaL6TwCRH7/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -Fx /tmp/BaL6TwCRH7/merge.a.bcf /tmp/BaL6TwCRH7/merge.b.bcf /tmp/BaL6TwCRH7/merge.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -Fx /tmp/BaL6TwCRH7/merge.a.bcf /tmp/BaL6TwCRH7/merge.b.bcf /tmp/BaL6TwCRH7/merge.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -0 /tmp/BaL6TwCRH7/merge.a.vcf.gz /tmp/BaL6TwCRH7/merge.b.vcf.gz /tmp/BaL6TwCRH7/merge.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -0 /tmp/BaL6TwCRH7/merge.a.vcf.gz /tmp/BaL6TwCRH7/merge.b.vcf.gz /tmp/BaL6TwCRH7/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -0 /tmp/BaL6TwCRH7/merge.a.bcf /tmp/BaL6TwCRH7/merge.b.bcf /tmp/BaL6TwCRH7/merge.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -0 /tmp/BaL6TwCRH7/merge.a.bcf /tmp/BaL6TwCRH7/merge.b.bcf /tmp/BaL6TwCRH7/merge.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m none /tmp/BaL6TwCRH7/merge.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.2.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m none /tmp/BaL6TwCRH7/merge.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m none /tmp/BaL6TwCRH7/merge.2.a.bcf /tmp/BaL6TwCRH7/merge.2.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m none /tmp/BaL6TwCRH7/merge.2.a.bcf /tmp/BaL6TwCRH7/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m both /tmp/BaL6TwCRH7/merge.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.2.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m both /tmp/BaL6TwCRH7/merge.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m both /tmp/BaL6TwCRH7/merge.2.a.bcf /tmp/BaL6TwCRH7/merge.2.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m both /tmp/BaL6TwCRH7/merge.2.a.bcf /tmp/BaL6TwCRH7/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m all /tmp/BaL6TwCRH7/merge.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.2.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m all /tmp/BaL6TwCRH7/merge.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m all /tmp/BaL6TwCRH7/merge.2.a.bcf /tmp/BaL6TwCRH7/merge.2.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m all /tmp/BaL6TwCRH7/merge.2.a.bcf /tmp/BaL6TwCRH7/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/BaL6TwCRH7/merge.3.a.vcf.gz /tmp/BaL6TwCRH7/merge.3.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/BaL6TwCRH7/merge.3.a.vcf.gz /tmp/BaL6TwCRH7/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/BaL6TwCRH7/merge.3.a.bcf /tmp/BaL6TwCRH7/merge.3.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/BaL6TwCRH7/merge.3.a.bcf /tmp/BaL6TwCRH7/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m id /tmp/BaL6TwCRH7/merge.4.a.vcf.gz /tmp/BaL6TwCRH7/merge.4.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m id /tmp/BaL6TwCRH7/merge.4.a.vcf.gz /tmp/BaL6TwCRH7/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples -m id /tmp/BaL6TwCRH7/merge.4.a.bcf /tmp/BaL6TwCRH7/merge.4.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m id /tmp/BaL6TwCRH7/merge.4.a.bcf /tmp/BaL6TwCRH7/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/gvcf.merge.1.vcf.gz /tmp/BaL6TwCRH7/gvcf.merge.2.vcf.gz /tmp/BaL6TwCRH7/gvcf.merge.3.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/gvcf.merge.1.vcf.gz /tmp/BaL6TwCRH7/gvcf.merge.2.vcf.gz /tmp/BaL6TwCRH7/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/gvcf.merge.1.bcf /tmp/BaL6TwCRH7/gvcf.merge.2.bcf /tmp/BaL6TwCRH7/gvcf.merge.3.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/gvcf.merge.1.bcf /tmp/BaL6TwCRH7/gvcf.merge.2.bcf /tmp/BaL6TwCRH7/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -m both,* /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -m both,** /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -i SRC:join /tmp/BaL6TwCRH7/merge.gvcf.3.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.3.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/BaL6TwCRH7/merge.gvcf.3.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.4.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.4.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.4.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.4.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.4.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.4.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.5.a.vcf.gz /tmp/BaL6TwCRH7/merge.5.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.5.a.vcf.gz /tmp/BaL6TwCRH7/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.5.a.bcf /tmp/BaL6TwCRH7/merge.5.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.5.a.bcf /tmp/BaL6TwCRH7/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.6.a.vcf.gz /tmp/BaL6TwCRH7/merge.6.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.6.a.vcf.gz /tmp/BaL6TwCRH7/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.6.a.bcf /tmp/BaL6TwCRH7/merge.6.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.6.a.bcf /tmp/BaL6TwCRH7/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.7.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.7.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.7.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.7.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.7.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.7.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.8.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.8.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.8.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.8.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.8.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.8.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/BaL6TwCRH7/merge.7.a.vcf.gz /tmp/BaL6TwCRH7/merge.7.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/BaL6TwCRH7/merge.7.a.vcf.gz /tmp/BaL6TwCRH7/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --force-samples /tmp/BaL6TwCRH7/merge.7.a.bcf /tmp/BaL6TwCRH7/merge.7.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/BaL6TwCRH7/merge.7.a.bcf /tmp/BaL6TwCRH7/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9e.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf /tmp/BaL6TwCRH7/merge.gvcf.9e.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf /tmp/BaL6TwCRH7/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9e.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9c.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9d.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf /tmp/BaL6TwCRH7/merge.gvcf.9e.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa -r 22:21-23 /tmp/BaL6TwCRH7/merge.gvcf.9a.bcf /tmp/BaL6TwCRH7/merge.gvcf.9b.bcf /tmp/BaL6TwCRH7/merge.gvcf.9c.bcf /tmp/BaL6TwCRH7/merge.gvcf.9d.bcf /tmp/BaL6TwCRH7/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -g /builddir/build/BUILD/bcftools-1.23/test/merge.gvcf.10.fa -m none /tmp/BaL6TwCRH7/merge.gvcf.10.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.noidx.a.vcf.gz /tmp/BaL6TwCRH7/merge.noidx.b.vcf.gz /tmp/BaL6TwCRH7/merge.noidx.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.noidx.a.vcf.gz /tmp/BaL6TwCRH7/merge.noidx.b.vcf.gz /tmp/BaL6TwCRH7/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.noidx.a.bcf /tmp/BaL6TwCRH7/merge.noidx.b.bcf /tmp/BaL6TwCRH7/merge.noidx.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.noidx.a.bcf /tmp/BaL6TwCRH7/merge.noidx.b.bcf /tmp/BaL6TwCRH7/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.c.vcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --no-index /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.23/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --no-index /tmp/BaL6TwCRH7/merge.noidx.a.bcf /tmp/BaL6TwCRH7/merge.noidx.b.bcf /tmp/BaL6TwCRH7/merge.noidx.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --no-index /tmp/BaL6TwCRH7/merge.noidx.a.bcf /tmp/BaL6TwCRH7/merge.noidx.b.bcf /tmp/BaL6TwCRH7/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.8.a.vcf.gz /tmp/BaL6TwCRH7/merge.8.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.8.a.vcf.gz /tmp/BaL6TwCRH7/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.8.a.bcf /tmp/BaL6TwCRH7/merge.8.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.8.a.bcf /tmp/BaL6TwCRH7/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.8.a.vcf.gz /tmp/BaL6TwCRH7/merge.8.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.8.a.vcf.gz /tmp/BaL6TwCRH7/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.8.a.bcf /tmp/BaL6TwCRH7/merge.8.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.8.a.bcf /tmp/BaL6TwCRH7/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.9.a.vcf.gz /tmp/BaL6TwCRH7/merge.9.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.9.a.vcf.gz /tmp/BaL6TwCRH7/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version  /tmp/BaL6TwCRH7/merge.9.a.bcf /tmp/BaL6TwCRH7/merge.9.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob  /tmp/BaL6TwCRH7/merge.9.a.bcf /tmp/BaL6TwCRH7/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.9.a.vcf.gz /tmp/BaL6TwCRH7/merge.9.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.9.a.vcf.gz /tmp/BaL6TwCRH7/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.9.a.bcf /tmp/BaL6TwCRH7/merge.9.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/BaL6TwCRH7/merge.9.a.bcf /tmp/BaL6TwCRH7/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/BaL6TwCRH7/merge.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/BaL6TwCRH7/merge.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m none /tmp/BaL6TwCRH7/merge.10.a.bcf /tmp/BaL6TwCRH7/merge.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/BaL6TwCRH7/merge.10.a.bcf /tmp/BaL6TwCRH7/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m both /tmp/BaL6TwCRH7/merge.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m both /tmp/BaL6TwCRH7/merge.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m both /tmp/BaL6TwCRH7/merge.10.a.bcf /tmp/BaL6TwCRH7/merge.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m both /tmp/BaL6TwCRH7/merge.10.a.bcf /tmp/BaL6TwCRH7/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m snp-ins-del /tmp/BaL6TwCRH7/merge.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.10.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m snp-ins-del /tmp/BaL6TwCRH7/merge.10.a.vcf.gz /tmp/BaL6TwCRH7/merge.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -m snp-ins-del /tmp/BaL6TwCRH7/merge.10.a.bcf /tmp/BaL6TwCRH7/merge.10.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m snp-ins-del /tmp/BaL6TwCRH7/merge.10.a.bcf /tmp/BaL6TwCRH7/merge.10.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.mrules.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.mrules.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.mrules.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.mrules.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.mrules.1.a.bcf /tmp/BaL6TwCRH7/merge.mrules.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.mrules.1.a.bcf /tmp/BaL6TwCRH7/merge.mrules.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/BaL6TwCRH7/merge.mrules.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.mrules.1.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/BaL6TwCRH7/merge.mrules.1.a.vcf.gz /tmp/BaL6TwCRH7/merge.mrules.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/BaL6TwCRH7/merge.mrules.1.a.bcf /tmp/BaL6TwCRH7/merge.mrules.1.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/BaL6TwCRH7/merge.mrules.1.a.bcf /tmp/BaL6TwCRH7/merge.mrules.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.5.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.5.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.5.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.5.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.5.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.5.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.5.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - --merge none /tmp/BaL6TwCRH7/merge.gvcf.5.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.5.b.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/BaL6TwCRH7/merge.gvcf.5.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - --merge none /tmp/BaL6TwCRH7/merge.gvcf.5.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.5.b.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/BaL6TwCRH7/merge.gvcf.5.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.5.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.11.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.11.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.11.c.vcf.gz
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.11.a.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.11.b.vcf.gz /tmp/BaL6TwCRH7/merge.gvcf.11.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.11.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.11.b.bcf /tmp/BaL6TwCRH7/merge.gvcf.11.c.bcf
.. ok

test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/BaL6TwCRH7/merge.gvcf.11.a.bcf /tmp/BaL6TwCRH7/merge.gvcf.11.b.bcf /tmp/BaL6TwCRH7/merge.gvcf.11.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version | grep -v ^##bcftools_
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' /tmp/BaL6TwCRH7/smpl-count.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1' /tmp/BaL6TwCRH7/smpl-count.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1 & GT="hom"' /tmp/BaL6TwCRH7/smpl-count.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1 & GT="hom"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'GT="hom" & smpl_count(LAA)==1' /tmp/BaL6TwCRH7/smpl-count.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/smpl-count.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'GT="hom" & smpl_count(LAA)==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]="."' /tmp/BaL6TwCRH7/query.filter.15.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]~"\."' /tmp/BaL6TwCRH7/query.filter.15.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]~"\."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!="."' /tmp/BaL6TwCRH7/query.filter.15.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' /tmp/BaL6TwCRH7/query.filter.15.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.15.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%TAG' -i 'TAG[*]!~"\."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' /tmp/BaL6TwCRH7/query.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' /tmp/BaL6TwCRH7/query.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' /tmp/BaL6TwCRH7/query.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' /tmp/BaL6TwCRH7/query.filter.14.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.14.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' /tmp/BaL6TwCRH7/query.filter.14.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.14.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' /tmp/BaL6TwCRH7/query.filter.14.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.14.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' /tmp/BaL6TwCRH7/query.func.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' /tmp/BaL6TwCRH7/query.func.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' /tmp/BaL6TwCRH7/query.func.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' /tmp/BaL6TwCRH7/query.func.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.func.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/BaL6TwCRH7/query.string.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/BaL6TwCRH7/query.string.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/BaL6TwCRH7/query.string.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.1.txt' /tmp/BaL6TwCRH7/query.string.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.string.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.1.txt'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.2.txt' /tmp/BaL6TwCRH7/query.string.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.string.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/builddir/build/BUILD/bcftools-1.23/test/query.string.2.2.txt'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%RSX\t%VKX\n' /tmp/BaL6TwCRH7/query.variantkey.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%RSX\t%VKX\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/BaL6TwCRH7/view.vectors.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/BaL6TwCRH7/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/BaL6TwCRH7/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/BaL6TwCRH7/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/BaL6TwCRH7/query.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/BaL6TwCRH7/query.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT="."'  -f'%POS %IINT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT="."'  -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT="."'  -f'%POS %IINT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IINT="."'  -f'%POS %IINT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/BaL6TwCRH7/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/BaL6TwCRH7/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/BaL6TwCRH7/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/BaL6TwCRH7/filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%LINE' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%LINE'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/BaL6TwCRH7/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/BaL6TwCRH7/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/BaL6TwCRH7/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/BaL6TwCRH7/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/BaL6TwCRH7/query.filter-type.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/BaL6TwCRH7/filter-missing-floats.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/BaL6TwCRH7/filter-missing-floats.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/BaL6TwCRH7/missing.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/BaL6TwCRH7/query.filter.2.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/BaL6TwCRH7/filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/BaL6TwCRH7/filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/BaL6TwCRH7/view.filter.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/BaL6TwCRH7/query.filter.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"' /tmp/BaL6TwCRH7/query.filter.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/BaL6TwCRH7/query.filter.3.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/BaL6TwCRH7/filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/BaL6TwCRH7/query.filter.4.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.56.out' /tmp/BaL6TwCRH7/view.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/view.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.56.out'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/BaL6TwCRH7/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/BaL6TwCRH7/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/BaL6TwCRH7/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/BaL6TwCRH7/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/BaL6TwCRH7/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/BaL6TwCRH7/query.filter.5.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B"  && FMT/TC[:GT]=="C"' /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B"  && FMT/TC[:GT]=="C"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.gtidx.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/BaL6TwCRH7/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/BaL6TwCRH7/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/BaL6TwCRH7/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/BaL6TwCRH7/query.negative.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/BaL6TwCRH7/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/BaL6TwCRH7/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/BaL6TwCRH7/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/BaL6TwCRH7/query.filter.11.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/BaL6TwCRH7/query.pbinom.1.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/BaL6TwCRH7/query.filter.6.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/BaL6TwCRH7/query.filter.7.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/BaL6TwCRH7/query.filter.8.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/BaL6TwCRH7/query.filter.8.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/BaL6TwCRH7/query.filter.9.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/BaL6TwCRH7/query.filter.9.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/BaL6TwCRH7/query.filter.13.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/BaL6TwCRH7/query.filter.10.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/BaL6TwCRH7/query.filter.10.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/BaL6TwCRH7/query.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/BaL6TwCRH7/query.filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/BaL6TwCRH7/query.filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/BaL6TwCRH7/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/BaL6TwCRH7/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/BaL6TwCRH7/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt /tmp/BaL6TwCRH7/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.23/test/query.smpl.11.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt /tmp/BaL6TwCRH7/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt /tmp/BaL6TwCRH7/query.smpl.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -l -S /builddir/build/BUILD/bcftools-1.23/test/query.smpl.txt
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/BaL6TwCRH7/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID~"s12"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/BaL6TwCRH7/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="rs123"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/BaL6TwCRH7/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID="abc"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt' /tmp/BaL6TwCRH7/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/BaL6TwCRH7/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!="abc"'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt' /tmp/BaL6TwCRH7/query.filter.id.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%ID\n' -i'ID!=@/builddir/build/BUILD/bcftools-1.23/test/query.filter.id.3.txt'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/BaL6TwCRH7/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/BaL6TwCRH7/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/BaL6TwCRH7/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER="A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/BaL6TwCRH7/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/BaL6TwCRH7/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/BaL6TwCRH7/filter.12.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/BaL6TwCRH7/filter.10.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'DP%10==2' -f'[ %DP]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/BaL6TwCRH7/filter.13.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/BaL6TwCRH7/query.header.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.header.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/BaL6TwCRH7/query.filter-or.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-or.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2'
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 |  DP=2' /tmp/BaL6TwCRH7/query.filter-or.vcf.gz
.. ok

test_vcf_query:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/query.filter-or.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 |  DP=2'
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s /tmp/BaL6TwCRH7/norm.check-ref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.check-ref.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s /tmp/BaL6TwCRH7/norm.check-ref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.check-ref.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/BaL6TwCRH7/norm.filter.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/BaL6TwCRH7/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/BaL6TwCRH7/norm.filter.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/BaL6TwCRH7/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/BaL6TwCRH7/norm.filter.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ID=@/builddir/build/BUILD/bcftools-1.23/test/norm.filter.txt' /tmp/BaL6TwCRH7/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/BaL6TwCRH7/norm.filter.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/BaL6TwCRH7/norm.filter.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c e /tmp/BaL6TwCRH7/norm.6.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c e /tmp/BaL6TwCRH7/norm.6.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.breakend.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.breakend.1.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.breakend.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.breakend.1.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.sort.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.sort.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -S lex /tmp/BaL6TwCRH7/norm.sort.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -S lex /tmp/BaL6TwCRH7/norm.sort.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/BaL6TwCRH7/norm.join-missing-ploidy.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/BaL6TwCRH7/norm.join-missing-ploidy.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/BaL6TwCRH7/norm.split.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/BaL6TwCRH7/norm.split.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version  /tmp/BaL6TwCRH7/norm.symbolic.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.3.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version  /tmp/BaL6TwCRH7/norm.symbolic.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -cx /tmp/BaL6TwCRH7/norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -cx /tmp/BaL6TwCRH7/norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --force /tmp/BaL6TwCRH7/norm.split.3.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --force /tmp/BaL6TwCRH7/norm.split.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --keep-sum AD /tmp/BaL6TwCRH7/norm.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --keep-sum AD /tmp/BaL6TwCRH7/norm.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/BaL6TwCRH7/norm.split.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/BaL6TwCRH7/norm.merge.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/BaL6TwCRH7/norm.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/BaL6TwCRH7/norm.merge.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/BaL6TwCRH7/norm.merge.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/BaL6TwCRH7/norm.merge.3.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/BaL6TwCRH7/norm.merge.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ -s /tmp/BaL6TwCRH7/norm.merge.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ -s /tmp/BaL6TwCRH7/norm.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -Nc s /tmp/BaL6TwCRH7/norm.setref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -Nc s /tmp/BaL6TwCRH7/norm.setref.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version /tmp/BaL6TwCRH7/norm.telomere.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version /tmp/BaL6TwCRH7/norm.telomere.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/BaL6TwCRH7/norm.rmdup.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d any /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d any /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/BaL6TwCRH7/norm.rmdup.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/BaL6TwCRH7/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/BaL6TwCRH7/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/BaL6TwCRH7/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/BaL6TwCRH7/norm.rmdup.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.rmdup.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/BaL6TwCRH7/norm.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/BaL6TwCRH7/norm.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.2.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/BaL6TwCRH7/norm.iupac.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.iupac.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/BaL6TwCRH7/norm.iupac.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.iupac.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/BaL6TwCRH7/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s --old-rec-tag XX /tmp/BaL6TwCRH7/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/BaL6TwCRH7/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/BaL6TwCRH7/norm.3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.3.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --force
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --force -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -a -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.1.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.2.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.2.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . /tmp/BaL6TwCRH7/atomize.split.3.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . /tmp/BaL6TwCRH7/atomize.split.3.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/BaL6TwCRH7/atomize.split.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/BaL6TwCRH7/atomize.split.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/BaL6TwCRH7/atomize.split.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/BaL6TwCRH7/atomize.split.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/BaL6TwCRH7/atomize.split.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/BaL6TwCRH7/norm.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/BaL6TwCRH7/norm.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/BaL6TwCRH7/norm.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/BaL6TwCRH7/norm.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/BaL6TwCRH7/norm.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/BaL6TwCRH7/norm.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/BaL6TwCRH7/norm.5.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/BaL6TwCRH7/norm.5.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/BaL6TwCRH7/norm.m-any.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/BaL6TwCRH7/norm.m-any.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/BaL6TwCRH7/norm.phased-split.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/BaL6TwCRH7/norm.phased-split.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/BaL6TwCRH7/norm.phased-join.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/BaL6TwCRH7/norm.phased-join.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/BaL6TwCRH7/norm.symbolic.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/BaL6TwCRH7/norm.symbolic.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/BaL6TwCRH7/norm.symbolic.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/BaL6TwCRH7/norm.symbolic.2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.symbolic.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/BaL6TwCRH7/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI /tmp/BaL6TwCRH7/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -g /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.gff /tmp/BaL6TwCRH7/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -g /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.gff /tmp/BaL6TwCRH7/norm.right-align.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.right-align.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/BaL6TwCRH7/norm.atom-split-norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.atom-split-norm.fa
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/BaL6TwCRH7/norm.atom-split-norm.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/norm.atom-split-norm.fa -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/BaL6TwCRH7/norm.string-tags.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/BaL6TwCRH7/norm.string-tags.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +indels
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +indels -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +snps -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -i 'type="snp"' /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -i 'type="snp"' /tmp/BaL6TwCRH7/norm.split.merge.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/BaL6TwCRH7/norm.merge.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/BaL6TwCRH7/norm.merge.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/BaL6TwCRH7/norm.merge.4.vcf.gz
.. ok

test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/BaL6TwCRH7/norm.merge.4.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'INFO/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/BaL6TwCRH7/filter.string.1.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'INFO/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/BaL6TwCRH7/filter.string.1.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'FMT/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/BaL6TwCRH7/filter.string.1.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'FMT/TAG=@/builddir/build/BUILD/bcftools-1.23/test/filter.string.1.txt' /tmp/BaL6TwCRH7/filter.string.1.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HA /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HAA /tmp/BaL6TwCRH7/merge.gvcf.2.a.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1:1-2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1:1-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1:1,1:2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1:1,1:2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1:1-1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r 1:1-1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1} | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}:1-2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}:1-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}:1-1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1}:1-1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1} | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}:1-2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}:1-1
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}-2
.. ok, expected non-zero status

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/weird-chr-names.vcf.gz -r {1:1-1}-2 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok, expected non-zero status

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -f PASS -Xks NA00003 /tmp/BaL6TwCRH7/view.vcf.gz -r20,Y
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -f PASS -Xks NA00003 /tmp/BaL6TwCRH7/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -xs NA00003 /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -xs NA00003 /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -p /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -p /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -P /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -P /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Hu /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -GVsnps /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -GVsnps /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -s ^NA00003 /tmp/BaL6TwCRH7/view.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -s ^NA00003 /tmp/BaL6TwCRH7/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version  /tmp/BaL6TwCRH7/view.omitgenotypes.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob  /tmp/BaL6TwCRH7/view.omitgenotypes.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -G /tmp/BaL6TwCRH7/view.omitgenotypes.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -G /tmp/BaL6TwCRH7/view.omitgenotypes.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HG /tmp/BaL6TwCRH7/view.omitgenotypes.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -a /tmp/BaL6TwCRH7/many.alleles.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -a /tmp/BaL6TwCRH7/many.alleles.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -asA /tmp/BaL6TwCRH7/view.vectors.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asA /tmp/BaL6TwCRH7/view.vectors.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -asB /tmp/BaL6TwCRH7/view.vectors.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asB /tmp/BaL6TwCRH7/view.vectors.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -asA /tmp/BaL6TwCRH7/view.vectors.2.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asA /tmp/BaL6TwCRH7/view.vectors.2.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/BaL6TwCRH7/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/BaL6TwCRH7/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/BaL6TwCRH7/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/BaL6TwCRH7/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'TXT0="text"' /tmp/BaL6TwCRH7/view.filter.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.23/test/view.chrs.tab /tmp/BaL6TwCRH7/view.chrs.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.23/test/view.chrs.tab /tmp/BaL6TwCRH7/view.chrs.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -i 'POS>=3062917' /tmp/BaL6TwCRH7/filter.2.vcf.gz 1:3062917-3157410
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'POS>=3062917' /tmp/BaL6TwCRH7/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/BaL6TwCRH7/idx.1.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/BaL6TwCRH7/idx.2.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.23/test/idx.2.bed /tmp/BaL6TwCRH7/idx.2.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.23/test/idx.3.bed /tmp/BaL6TwCRH7/idx.3.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.23/test/idx.4.bed /tmp/BaL6TwCRH7/idx.4.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ht 2 /tmp/BaL6TwCRH7/view-t.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ht 3 /tmp/BaL6TwCRH7/view-t.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/BaL6TwCRH7/overlap.vcf.gz 
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.1.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.1.vcf     | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.2.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.2.vcf     | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.3.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.3.vcf     | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.4.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.4.vcf     | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.5.vcf -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.5.vcf     | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.23/bcftools view /builddir/build/BUILD/bcftools-1.23/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -C5:nonmajor /tmp/BaL6TwCRH7/view.minmaxac.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -c6:nonmajor /tmp/BaL6TwCRH7/view.minmaxac.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -q0.3:major /tmp/BaL6TwCRH7/view.minmaxac.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/BaL6TwCRH7/view.filter.annovar.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/BaL6TwCRH7/view.filter.annovar.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/BaL6TwCRH7/view.filter.annovar.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -a /tmp/BaL6TwCRH7/view-a.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt /tmp/BaL6TwCRH7/view.sites.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt /tmp/BaL6TwCRH7/view.sites.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt.gz /tmp/BaL6TwCRH7/view.sites.vcf.gz 
.. ok

test_vcf_view:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.23/test/view.sites.txt.gz /tmp/BaL6TwCRH7/view.sites.vcf.gz  | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -s0 /tmp/BaL6TwCRH7/mpileup.2.vcf.gz
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/BaL6TwCRH7/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools head -s0
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -s1 /tmp/BaL6TwCRH7/mpileup.2.vcf.gz
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/BaL6TwCRH7/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools head -s1
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.23/bcftools head -s2 -h2 /tmp/BaL6TwCRH7/mpileup.2.vcf.gz
.. ok

test_vcf_head2:
	/builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/BaL6TwCRH7/mpileup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools head -s2 -h2
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s sample1 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s sample1 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s ^sample2,sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s ^sample2,sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s sample3 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -s ^sample1,sample2 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -s ^sample1,sample2 /builddir/build/BUILD/bcftools-1.23/test/samples.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.txt -S /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.ped /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.txt -S /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.ped /builddir/build/BUILD/bcftools-1.23/test/call-ploidy.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.2.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.2.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.23/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.cals.1.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.1.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.cals.1.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.cals.2.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.2.vcf
.. ok

test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mA -C alleles -T /tmp/BaL6TwCRH7/mpileup.cals.2.tab.gz  /builddir/build/BUILD/bcftools-1.23/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.ped /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.23/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.23/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.23/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.23/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.23/test/call-G.2.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.23/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf
.. ok

test_vcf_call:
	/builddir/build/BUILD/bcftools-1.23/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.23/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.2.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.23/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.23/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.23/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%GT]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%FR]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%FR]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS[\t%AD]\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%QUAL\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.23/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\t%QUAL\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.23/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%POS\n'
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.23/test/filter.7.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.23/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.23/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.23/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.23/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | grep -v ^##bcftools_
.. ok

test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.23/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.23/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.23/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.23/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.23/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.23/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.23/test/sort.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | /builddir/build/BUILD/bcftools-1.23/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.23/test/regions.tab /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.23/test/regions.tab
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.23/test/regions.tab /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/BaL6TwCRH7/regions.tab.gz /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/BaL6TwCRH7/regions.tab.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/BaL6TwCRH7/regions.tab.gz /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/BaL6TwCRH7/regions.bed /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/BaL6TwCRH7/regions.bed
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/BaL6TwCRH7/regions.bed /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/BaL6TwCRH7/regions.bed.gz /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/BaL6TwCRH7/regions.bed.gz
.. ok

test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/BaL6TwCRH7/regions.bed.gz /tmp/BaL6TwCRH7/regions.vcf.gz
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots36.bed.gz  -c CHROM,POS,-,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots36.bed.gz  -c CHROM,POS,-,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots36.bed.gz  -c CHROM,BEG,END,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots36.bed.gz  -c CHROM,BEG,END,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /builddir/build/BUILD/bcftools-1.23/test/annotate36.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots35.vcf.gz  -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/BaL6TwCRH7/annotate35.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots35.vcf.gz  -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/BaL6TwCRH7/annotate35.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.escape.1.tab.gz  -c CHROM,POS,ISTR,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate.escape.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.escape.1.tab.gz  -c CHROM,POS,ISTR,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate.escape.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.match.1.tab.gz  -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.match.1.tab.gz  -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.match.1.tab.gz  -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.match.1.tab.gz  -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.match.1.tab.gz  -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.match.1.tab.gz  -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /builddir/build/BUILD/bcftools-1.23/test/annotate.match.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/BaL6TwCRH7/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/BaL6TwCRH7/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -x FORMAT /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -x FORMAT /builddir/build/BUILD/bcftools-1.23/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots4.vcf.gz  -c +INFO /tmp/BaL6TwCRH7/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots4.vcf.gz  -c +INFO /tmp/BaL6TwCRH7/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.23/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.23/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.23/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.23/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.23/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots11.vcf.gz  -c FMT /tmp/BaL6TwCRH7/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots11.vcf.gz  -c FMT /tmp/BaL6TwCRH7/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/BaL6TwCRH7/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.23/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.23/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.23/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.23/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate15.tab.gz  -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">' /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate15.tab.gz  -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">' /builddir/build/BUILD/bcftools-1.23/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -x FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -x FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.23/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate18.1.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.23/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate18.1.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.23/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate18.2.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.23/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate18.2.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.23/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -c INFO/FILTER:=FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate19.dst.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -c INFO/FILTER:=FILTER /builddir/build/BUILD/bcftools-1.23/test/annotate19.dst.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/BaL6TwCRH7/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate20.src.vcf.gz  -c  FMT/GT /tmp/BaL6TwCRH7/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate20.src.vcf.gz  -c  FMT/GT /tmp/BaL6TwCRH7/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate20.src.vcf.gz  -c +FMT/GT /tmp/BaL6TwCRH7/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate20.src.vcf.gz  -c +FMT/GT /tmp/BaL6TwCRH7/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate20.src.vcf.gz  -c -FMT/GT /tmp/BaL6TwCRH7/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate20.src.vcf.gz  -c -FMT/GT /tmp/BaL6TwCRH7/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.23/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.23/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing-append.tab.gz  -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.23/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing-append.tab.gz  -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.23/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.23/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.23/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   --rename-annots /builddir/build/BUILD/bcftools-1.23/test/annotate21.txt /builddir/build/BUILD/bcftools-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   --rename-annots /builddir/build/BUILD/bcftools-1.23/test/annotate21.txt /builddir/build/BUILD/bcftools-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.23/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/BaL6TwCRH7/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/BaL6TwCRH7/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate24.src.vcf.gz  -c XX /tmp/BaL6TwCRH7/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate24.src.vcf.gz  -c XX /tmp/BaL6TwCRH7/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.23/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate26.tab.gz  -c CHROM,POS,-POS /builddir/build/BUILD/bcftools-1.23/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate26.tab.gz  -c CHROM,POS,-POS /builddir/build/BUILD/bcftools-1.23/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.23/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.id.vcf.gz  -c ALT /tmp/BaL6TwCRH7/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.id.vcf.gz  -c ALT /tmp/BaL6TwCRH7/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.id.vcf.gz  -c +ALT /tmp/BaL6TwCRH7/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.id.vcf.gz  -c +ALT /tmp/BaL6TwCRH7/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/BaL6TwCRH7/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/BaL6TwCRH7/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/BaL6TwCRH7/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/BaL6TwCRH7/annotate.id.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /builddir/build/BUILD/bcftools-1.23/test/annotate27.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /builddir/build/BUILD/bcftools-1.23/test/annotate27.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /builddir/build/BUILD/bcftools-1.23/test/annotate28.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate   -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob   -m XXX /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots34.tab.gz  -c CHROM,FROM,TO,INFO/END -H '##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate in reference for SV">' /builddir/build/BUILD/bcftools-1.23/test/annotate34.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots34.tab.gz  -c CHROM,FROM,TO,INFO/END -H '##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate in reference for SV">' /builddir/build/BUILD/bcftools-1.23/test/annotate34.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/BaL6TwCRH7/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /builddir/build/BUILD/bcftools-1.23/test/annots-mark.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate -Ob -a /tmp/BaL6TwCRH7/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /builddir/build/BUILD/bcftools-1.23/test/annots-mark.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/BaL6TwCRH7/checkploidy.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/BaL6TwCRH7/checkploidy.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/BaL6TwCRH7/checkploidy.2.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/BaL6TwCRH7/checkploidy.2.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/BaL6TwCRH7/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +check-ploidy --no-version /tmp/BaL6TwCRH7/checkploidy.2.bcf -- -m | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +missing2ref --no-version /tmp/BaL6TwCRH7/plugin1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +missing2ref --no-version /tmp/BaL6TwCRH7/plugin1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.23/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.2.vcf.gz -- -t a -n i | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.2.bcf -- -t a -n i | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.vcf.gz -i 'GT="mis"' -- -t . -nc:././. | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.3.bcf -i 'GT="mis"' -- -t . -nc:././. | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.5.vcf.gz -- -t a -n X | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] AD should be declared as Number=R
[W::bcf_hdr_check_sanity] AD should be declared as Number=R
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.5.bcf -- -t a -n X | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.5.vcf.gz -- -t a -n c:0/X/X | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] AD should be declared as Number=R
[W::bcf_hdr_check_sanity] AD should be declared as Number=R
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.5.bcf -- -t a -n c:0/X/X | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.6.vcf.gz -- -t ./x -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.6.bcf -- -t ./x -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.6.vcf.gz -- -t . -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.6.bcf -- -t . -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.6.vcf.gz -- -t r:0.5 -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +setGT --no-version /tmp/BaL6TwCRH7/setGT.6.bcf -- -t r:0.5 -n . | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-AN-AC --no-version /tmp/BaL6TwCRH7/plugin1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-AN-AC --no-version /tmp/BaL6TwCRH7/plugin1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/BaL6TwCRH7/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/BaL6TwCRH7/dosage.bcf -- -t PL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/BaL6TwCRH7/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/BaL6TwCRH7/dosage.bcf -- -t GL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/BaL6TwCRH7/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +dosage /tmp/BaL6TwCRH7/dosage.bcf -- -t GT | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixploidy --no-version /tmp/BaL6TwCRH7/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.23/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.23/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixploidy --no-version /tmp/BaL6TwCRH7/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.23/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.23/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/BaL6TwCRH7/view.PL.vcf.gz -v -rX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/BaL6TwCRH7/view.PL.bcf -v -rX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/BaL6TwCRH7/view.GL.vcf.gz -v -rX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +guess-ploidy /tmp/BaL6TwCRH7/view.GL.bcf -v -rX | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/view.GL.vcf.gz -- --gl-to-gp | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/view.GL.bcf -- --gl-to-gp | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/tag2tag.LPL.1.bcf -- --LXX-to-XX | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX -r | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/tag2tag.LPL.1.bcf -- --LXX-to-XX -r | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/tag2tag.LPL.1.vcf.gz -- --LXX-to-XX -r -d AD:0,PL:255 -s 3 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +tag2tag --no-version /tmp/BaL6TwCRH7/tag2tag.LPL.1.bcf -- --LXX-to-XX -r -d AD:0,PL:255 -s 3 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +add-variantkey /tmp/BaL6TwCRH7/query.variantkey.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +add-variantkey /tmp/BaL6TwCRH7/query.variantkey.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variantkey-hex /tmp/BaL6TwCRH7/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variantkey-hex /tmp/BaL6TwCRH7/query.variantkey.bcf test/ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +allele-length /tmp/BaL6TwCRH7/query.nucleotide.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +allele-length /tmp/BaL6TwCRH7/query.nucleotide.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/query.func.1.vcf.gz -- -t 'FMT/AB:1=float(FMT/AD[*:0] / ssum(FMT/AD[*]))' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/query.func.1.bcf -- -t 'FMT/AB:1=float(FMT/AD[*:0] / ssum(FMT/AD[*]))' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fmissing.vcf.gz -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fmissing.bcf -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fmissing.vcf.gz -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING:1=F_PASS(GT="mis")' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fmissing.bcf -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'F_MISSING:1=F_PASS(GT="mis")' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fmissing.vcf.gz -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'N_MISSING:1=int(N_PASS(GT="mis"))' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fmissing.bcf -- -S /builddir/build/BUILD/bcftools-1.23/test/fmissing.txt -t 'N_MISSING:1=int(N_PASS(GT="mis"))' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.vcf.gz -- -t 'FT:1=phred(fisher(INFO/DP4))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.bcf -- -t 'FT:1=phred(fisher(INFO/DP4))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.vcf.gz -- -t 'FT:1=phred(fisher(INFO/ADF[0,2],INFO/ADR[0,2]))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.bcf -- -t 'FT:1=phred(fisher(INFO/ADF[0,2],INFO/ADR[0,2]))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.vcf.gz -- -t 'FT:1=phred(fisher(INFO/ADF,INFO/ADR))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.bcf -- -t 'FT:1=phred(fisher(INFO/ADF,INFO/ADR))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.vcf.gz -- -t 'FMT/FT:1=phred(fisher(FMT/DP4))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.bcf -- -t 'FMT/FT:1=phred(fisher(FMT/DP4))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.vcf.gz -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF,FORMAT/ADR))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.bcf -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF,FORMAT/ADR))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.vcf.gz -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF[:0,1],FORMAT/ADR[:0,1]))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fisher.bcf -- -t 'FMT/FT:1=phred(fisher(FORMAT/ADF[:0,1],FORMAT/ADR[:0,1]))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.23/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hemi.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hemi.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hwe.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hwe.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-rw.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-rw.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.vcf.gz -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.vcf.gz -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.bcf -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.vcf.gz -- -t 'good=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])>=1e-5)','bad=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])<1e-5)' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-tags --no-version /tmp/BaL6TwCRH7/fill-tags-AD.bcf -- -t 'good=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])>=1e-5)','bad=N_PASS(binom(FMT/AD[:0],FMT/AD[:1])<1e-5)' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz  | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTisec /tmp/BaL6TwCRH7/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-switch-rate /tmp/BaL6TwCRH7/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.23/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-switch-rate /tmp/BaL6TwCRH7/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.23/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/BaL6TwCRH7/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/BaL6TwCRH7/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/BaL6TwCRH7/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-stats /tmp/BaL6TwCRH7/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +smpl-stats /tmp/BaL6TwCRH7/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +smpl-stats /tmp/BaL6TwCRH7/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/BaL6TwCRH7/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/BaL6TwCRH7/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/BaL6TwCRH7/indel-stats.vcf.gz  -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/BaL6TwCRH7/indel-stats.bcf  -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/BaL6TwCRH7/indel-stats.vcf.gz  -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +indel-stats /tmp/BaL6TwCRH7/indel-stats.bcf  -p /builddir/build/BUILD/bcftools-1.23/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +ad-bias /tmp/BaL6TwCRH7/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.23/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +af-dist /tmp/BaL6TwCRH7/af-dist.vcf.gz  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +af-dist /tmp/BaL6TwCRH7/af-dist.bcf  | grep -v bcftools | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -i /tmp/BaL6TwCRH7/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -i /tmp/BaL6TwCRH7/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip-all | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m flip-all | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m swap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fixref /tmp/BaL6TwCRH7/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -m swap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/BaL6TwCRH7/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.23/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/BaL6TwCRH7/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.23/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/BaL6TwCRH7/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/BaL6TwCRH7/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/BaL6TwCRH7/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +fill-from-fasta /tmp/BaL6TwCRH7/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/BaL6TwCRH7/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/BaL6TwCRH7/view.bcf -- -s NA00001 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/BaL6TwCRH7/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/BaL6TwCRH7/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/BaL6TwCRH7/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok

[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
[W::bcf_hdr_check_sanity] MQ should be declared as Type=Float
test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +GTsubset --no-version /tmp/BaL6TwCRH7/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.vcf.gz -p child1,dad1,mom1 -md | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.bcf -p child1,dad1,mom1 -md | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.vcf.gz -p child1,dad1,mom1 -mg | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.bcf -p child1,dad1,mom1 -mg | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.vcf.gz -p child1,dad1,mom1 -me | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.bcf -p child1,dad1,mom1 -me | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.vcf.gz -p child1,dad1,mom1 -ma | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.bcf -p child1,dad1,mom1 -ma | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.vcf.gz -p child1,dad1,mom1 -mm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.bcf -p child1,dad1,mom1 -mm | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.vcf.gz -p child1,dad1,mom1 | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +mendelian2 /tmp/BaL6TwCRH7/mendelian.bcf -p child1,dad1,mom1 | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.23/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.23/test/contrast1.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.23/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.23/test/contrast1.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +contrast /tmp/BaL6TwCRH7/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother           | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.bcf -p proband,father,mother           | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.4.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.5.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.6.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother        --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.7.bcf -p proband,father,mother        --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother  | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.8.bcf -p proband,father,mother  | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.11.vcf.gz -p 1X:proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS  DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.11.bcf -p 1X:proband,father,mother | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS  DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.11.vcf.gz -p 1X:proband,father,mother --strictly-novel | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS  DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +trio-dnm2 /tmp/BaL6TwCRH7/trio-dnm/trio-dnm.11.bcf -p 1X:proband,father,mother --strictly-novel | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM:%POS  DNM=[%DNM ]\tAD=[%AD ]\tQS=[%QS ]\tVAF=[%VAF ]\tVA=[%VA ]' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/BaL6TwCRH7/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/BaL6TwCRH7/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/BaL6TwCRH7/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/BaL6TwCRH7/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/BaL6TwCRH7/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +gvcfz /tmp/BaL6TwCRH7/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.vcf.gz -m overlap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.bcf -m overlap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.vcf.gz -m overlap -M overlap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.bcf -m overlap -M overlap | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.vcf.gz -m overlap -O t | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.bcf -m overlap -O t | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.vcf.gz -m overlap --reverse | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.bcf -m overlap --reverse | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.vcf.gz -m dup -M DUP | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.bcf -m dup -M DUP | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.vcf.gz -m dup -M unique --reverse | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.1.bcf -m dup -M unique --reverse | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.2.vcf.gz -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.2.bcf -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.3.vcf.gz -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.3.bcf -m 'min(QUAL)' -M rmme | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.3.vcf.gz -m 'min(QUAL)' -M rmme --missing 0 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.3.bcf -m 'min(QUAL)' -M rmme --missing 0 | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.3.vcf.gz -m 'min(QUAL)' -M rmme --missing DP | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +remove-overlaps /tmp/BaL6TwCRH7/remove-overlaps.3.bcf -m 'min(QUAL)' -M rmme --missing DP | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -c Consequence -s worst:missense+:worst | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s worst:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s worst:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s CANONICAL=YES:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s CANONICAL=YES:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s primary:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s primary:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s CANONICAL=YES:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s CANONICAL=YES:missense+:worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -s CANONICAL=YES:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -s CANONICAL=YES:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.bcf -s worst -f'%POS\t%AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' -a BCSQ | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.3.vcf.gz -s worst::worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.3.bcf -s worst::worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.3.vcf.gz -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.3.bcf -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -H | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -H | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -HH | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d -HH | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A @@@ -d -H | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A @@@ -d -H | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n'         -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.bcf -f '%POS\t%BCSQ\n'         -A tab -d | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d -s ::worst | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d -s ::worst | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n'         -A tab -d -s ::worst | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.4.bcf -f '%POS\t%BCSQ\n'         -A tab -d -s ::worst | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM          | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM          | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.5.vcf.gz -s :synonymous    -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.5.bcf -s :synonymous    -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.vcf.gz         -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.bcf         -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.vcf.gz -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.bcf -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.vcf.gz         -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.8.bcf         -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.9.vcf.gz -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.9.bcf -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.10.vcf.gz -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.10.bcf -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.10.vcf.gz -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.10.bcf -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.10.vcf.gz        -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.10.bcf        -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g /builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.gene-list.txt | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.vcf.gz -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.gene-list.bcf -d -f '%CHROM:%POS %Gene %Consequence\n' -g +/builddir/build/BUILD/bcftools-1.23/test/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.broken-LoF.vcf.gz -d -f '%CHROM:%POS %Consequence %LoF_info\n' -a vep | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.broken-LoF.bcf -d -f '%CHROM:%POS %Consequence %LoF_info\n' -a vep | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.broken-LoF.vcf.gz -d -f '%CHROM:%POS %LoF_info\n' -a vep -i 'Consequence=="frameshift_variant"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.broken-LoF.bcf -d -f '%CHROM:%POS %LoF_info\n' -a vep -i 'Consequence=="frameshift_variant"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -f'%POS\n' -i'SYMBOL~"SAMD11"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -f'%POS\n' -i'SYMBOL~"SAMD11"' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.vcf.gz -f'%POS\t%MAX_AF\n' -i'MAX_AF>0.999' -c MAX_AF,MAX_AF:float,MAX_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.bcf -f'%POS\t%MAX_AF\n' -i'MAX_AF>0.999' -c MAX_AF,MAX_AF:float,MAX_AF | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter.vcf.gz -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter.bcf -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter.vcf.gz -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE %CSQ' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter.bcf -s worst -i'CSQ~"nonsense"' -f '%POS %Consequence %Feature %BIOTYPE %CSQ' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL!=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL!=YES | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL= | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s CANONICAL= | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s MANE_SELECT!='' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -f '%POS %CANONICAL %MANE_SELECT %Consequence' -s MANE_SELECT!='' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -s mane | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -s primary | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.vcf.gz -s PolyPhen~damaging | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.select-tr-expr.bcf -s PolyPhen~damaging | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.types.vcf.gz -f'%cDNA_position %CDS_position %Protein_position' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.types.bcf -f'%cDNA_position %CDS_position %Protein_position' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.types.vcf.gz -f'%cDNA_position %CDS_position %Protein_position' -c cDNA_position:int,CDS_position:int,Protein_position:int | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.types.bcf -f'%cDNA_position %CDS_position %Protein_position' -c cDNA_position:int,CDS_position:int,Protein_position:int | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter-missing-bt2098.vcf.gz -e 'gnomad_genomes_AF >= 0.02' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter-missing-bt2098.bcf -e 'gnomad_genomes_AF >= 0.02' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter-missing-bt2098.vcf.gz -i 'gnomad_genomes_AF < 0.02 || gnomad_genomes_AF=="."' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split-vep /tmp/BaL6TwCRH7/split-vep.filter-missing-bt2098.bcf -i 'gnomad_genomes_AF < 0.02 || gnomad_genomes_AF=="."' | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS 	 %gnomad_genomes_AF
' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +parental-origin /tmp/BaL6TwCRH7/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/BaL6TwCRH7/prune.2.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 1 -a r2,LD,HD /tmp/BaL6TwCRH7/prune.2.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5  /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2 -a r2 -m 0.5  /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N 1st /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N 1st /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/BaL6TwCRH7/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/BaL6TwCRH7/prune.1.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' -k /tmp/BaL6TwCRH7/prune.3.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' -k /tmp/BaL6TwCRH7/prune.3.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' /tmp/BaL6TwCRH7/prune.3.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -a count -i 'XX!=0' /tmp/BaL6TwCRH7/prune.3.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -m count=2 -i 'XX!=0' /tmp/BaL6TwCRH7/prune.3.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +prune -w 3bp -m count=2 -i 'XX!=0' /tmp/BaL6TwCRH7/prune.3.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance /tmp/BaL6TwCRH7/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance /tmp/BaL6TwCRH7/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d nearest /tmp/BaL6TwCRH7/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d nearest /tmp/BaL6TwCRH7/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d fwd /tmp/BaL6TwCRH7/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d fwd /tmp/BaL6TwCRH7/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d rev /tmp/BaL6TwCRH7/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d rev /tmp/BaL6TwCRH7/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d both /tmp/BaL6TwCRH7/variant-distance.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +variant-distance -d both /tmp/BaL6TwCRH7/variant-distance.bcf  | grep -v ^##bcftools_
.. ok

test_plugin_vrfs:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vrfs -a /tmp/BaL6TwCRH7/mpileup.bam.list -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -s /builddir/build/BUILD/bcftools-1.23/test/vrfs.sites.txt | sort
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.1   && cd /tmp/BaL6TwCRH7/split.1.1  && for f in A1.vcf A2.vcf A3.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.2 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.2.txt  && cd /tmp/BaL6TwCRH7/split.1.2  && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.3 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt  && cd /tmp/BaL6TwCRH7/split.1.3  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.4 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt -i 'GT[0]="alt"'  && cd /tmp/BaL6TwCRH7/split.1.4  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.5 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt -i 'GT="alt"'  && cd /tmp/BaL6TwCRH7/split.1.5  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.6 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.4.txt -i 'GT="alt"'  && cd /tmp/BaL6TwCRH7/split.1.6  && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.1.vcf -o /tmp/BaL6TwCRH7/split.1.7 -G /builddir/build/BUILD/bcftools-1.23/test/split.grp.1.1.txt  && cd /tmp/BaL6TwCRH7/split.1.7  && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_split:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +split /builddir/build/BUILD/bcftools-1.23/test/split.2.vcf -o /tmp/BaL6TwCRH7/split.2.1   && cd /tmp/BaL6TwCRH7/split.2.1  && for f in A1_A1-1.vcf A1_A1-2.vcf A1_A1.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.23/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.23/bcftools view -H $f; done
.. ok

test_plugin_scatter:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +scatter /builddir/build/BUILD/bcftools-1.23/test/scatter.1.vcf -o /tmp/BaL6TwCRH7/scatter.1.1 -n 3 && cd /tmp/BaL6TwCRH7/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^##
.. ok

test_plugin_scatter:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +scatter /builddir/build/BUILD/bcftools-1.23/test/scatter.1.vcf -o /tmp/BaL6TwCRH7/scatter.1.2 -s 21,22 && cd /tmp/BaL6TwCRH7/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^##
.. ok

test_plugin_scatter:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +scatter /builddir/build/BUILD/bcftools-1.23/test/scatter.1.vcf -o /tmp/BaL6TwCRH7/scatter.1.3 -s 21,22 -x X && cd /tmp/BaL6TwCRH7/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^##
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G  /tmp/BaL6TwCRH7/concat.1.a.vcf.gz /tmp/BaL6TwCRH7/concat.1.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G  /tmp/BaL6TwCRH7/concat.1.a.vcf.gz /tmp/BaL6TwCRH7/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G  /builddir/build/BUILD/bcftools-1.23/test/concat.1.a.vcf /builddir/build/BUILD/bcftools-1.23/test/concat.1.b.vcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version   /tmp/BaL6TwCRH7/concat.1.a.vcf.gz /tmp/BaL6TwCRH7/concat.1.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob   /tmp/BaL6TwCRH7/concat.1.a.vcf.gz /tmp/BaL6TwCRH7/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version   /builddir/build/BUILD/bcftools-1.23/test/concat.1.a.vcf /builddir/build/BUILD/bcftools-1.23/test/concat.1.b.vcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version   /tmp/BaL6TwCRH7/concat.1.a.bcf /tmp/BaL6TwCRH7/concat.1.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob   /tmp/BaL6TwCRH7/concat.1.a.bcf /tmp/BaL6TwCRH7/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -a  /tmp/BaL6TwCRH7/concat.2.a.vcf.gz /tmp/BaL6TwCRH7/concat.2.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -a  /tmp/BaL6TwCRH7/concat.2.a.vcf.gz /tmp/BaL6TwCRH7/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -a  /tmp/BaL6TwCRH7/concat.2.a.bcf /tmp/BaL6TwCRH7/concat.2.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -a  /tmp/BaL6TwCRH7/concat.2.a.bcf /tmp/BaL6TwCRH7/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -aD  /tmp/BaL6TwCRH7/concat.2.a.vcf.gz /tmp/BaL6TwCRH7/concat.2.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -aD  /tmp/BaL6TwCRH7/concat.2.a.vcf.gz /tmp/BaL6TwCRH7/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -aD  /tmp/BaL6TwCRH7/concat.2.a.bcf /tmp/BaL6TwCRH7/concat.2.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -aD  /tmp/BaL6TwCRH7/concat.2.a.bcf /tmp/BaL6TwCRH7/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn  /tmp/BaL6TwCRH7/concat.3.a.vcf.gz /tmp/BaL6TwCRH7/concat.3.b.vcf.gz /tmp/BaL6TwCRH7/concat.3.0.vcf.gz /tmp/BaL6TwCRH7/concat.3.c.vcf.gz /tmp/BaL6TwCRH7/concat.3.d.vcf.gz /tmp/BaL6TwCRH7/concat.3.e.vcf.gz /tmp/BaL6TwCRH7/concat.3.f.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn  /tmp/BaL6TwCRH7/concat.3.a.vcf.gz /tmp/BaL6TwCRH7/concat.3.b.vcf.gz /tmp/BaL6TwCRH7/concat.3.0.vcf.gz /tmp/BaL6TwCRH7/concat.3.c.vcf.gz /tmp/BaL6TwCRH7/concat.3.d.vcf.gz /tmp/BaL6TwCRH7/concat.3.e.vcf.gz /tmp/BaL6TwCRH7/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn  /tmp/BaL6TwCRH7/concat.3.a.bcf /tmp/BaL6TwCRH7/concat.3.b.bcf /tmp/BaL6TwCRH7/concat.3.0.bcf /tmp/BaL6TwCRH7/concat.3.c.bcf /tmp/BaL6TwCRH7/concat.3.d.bcf /tmp/BaL6TwCRH7/concat.3.e.bcf /tmp/BaL6TwCRH7/concat.3.f.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn  /tmp/BaL6TwCRH7/concat.3.a.bcf /tmp/BaL6TwCRH7/concat.3.b.bcf /tmp/BaL6TwCRH7/concat.3.0.bcf /tmp/BaL6TwCRH7/concat.3.c.bcf /tmp/BaL6TwCRH7/concat.3.d.bcf /tmp/BaL6TwCRH7/concat.3.e.bcf /tmp/BaL6TwCRH7/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
Random seed for test_naive_concat: 2288247141
.. ok

test_naive_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --naive-force /tmp/BaL6TwCRH7/naive_concat.0.bcf /tmp/BaL6TwCRH7/naive_concat.1.bcf /tmp/BaL6TwCRH7/naive_concat.2.bcf /tmp/BaL6TwCRH7/naive_concat.3.bcf /tmp/BaL6TwCRH7/naive_concat.4.bcf /tmp/BaL6TwCRH7/naive_concat.5.bcf /tmp/BaL6TwCRH7/naive_concat.6.bcf /tmp/BaL6TwCRH7/naive_concat.7.bcf /tmp/BaL6TwCRH7/naive_concat.8.bcf /tmp/BaL6TwCRH7/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_naive_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --naive /tmp/BaL6TwCRH7/naive_concat.0.vcf.gz /tmp/BaL6TwCRH7/naive_concat.1.vcf.gz /tmp/BaL6TwCRH7/naive_concat.2.vcf.gz /tmp/BaL6TwCRH7/naive_concat.3.vcf.gz /tmp/BaL6TwCRH7/naive_concat.4.vcf.gz /tmp/BaL6TwCRH7/naive_concat.5.vcf.gz /tmp/BaL6TwCRH7/naive_concat.6.vcf.gz /tmp/BaL6TwCRH7/naive_concat.7.vcf.gz /tmp/BaL6TwCRH7/naive_concat.8.vcf.gz /tmp/BaL6TwCRH7/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view -H
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l  /tmp/BaL6TwCRH7/concat.4.a.vcf.gz /tmp/BaL6TwCRH7/concat.4.b.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l  /tmp/BaL6TwCRH7/concat.4.a.vcf.gz /tmp/BaL6TwCRH7/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l  /tmp/BaL6TwCRH7/concat.4.a.bcf /tmp/BaL6TwCRH7/concat.4.b.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l  /tmp/BaL6TwCRH7/concat.4.a.bcf /tmp/BaL6TwCRH7/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn  /tmp/BaL6TwCRH7/concat.5.a.vcf.gz /tmp/BaL6TwCRH7/concat.5.b.vcf.gz /tmp/BaL6TwCRH7/concat.5.c.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn  /tmp/BaL6TwCRH7/concat.5.a.vcf.gz /tmp/BaL6TwCRH7/concat.5.b.vcf.gz /tmp/BaL6TwCRH7/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-warn  /tmp/BaL6TwCRH7/concat.5.a.bcf /tmp/BaL6TwCRH7/concat.5.b.bcf /tmp/BaL6TwCRH7/concat.5.c.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn  /tmp/BaL6TwCRH7/concat.5.a.bcf /tmp/BaL6TwCRH7/concat.5.b.bcf /tmp/BaL6TwCRH7/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -l --ligate-force  /tmp/BaL6TwCRH7/concat.5.a.bcf /tmp/BaL6TwCRH7/concat.5.b.bcf /tmp/BaL6TwCRH7/concat.5.c.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-force  /tmp/BaL6TwCRH7/concat.5.a.bcf /tmp/BaL6TwCRH7/concat.5.b.bcf /tmp/BaL6TwCRH7/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G -a -D  /tmp/BaL6TwCRH7/concat.5.a.vcf.gz /tmp/BaL6TwCRH7/concat.5.b.vcf.gz /tmp/BaL6TwCRH7/concat.5.c.vcf.gz
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G -a -D  /tmp/BaL6TwCRH7/concat.5.a.vcf.gz /tmp/BaL6TwCRH7/concat.5.b.vcf.gz /tmp/BaL6TwCRH7/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat --no-version -G -a -D  /tmp/BaL6TwCRH7/concat.5.a.bcf /tmp/BaL6TwCRH7/concat.5.b.bcf /tmp/BaL6TwCRH7/concat.5.c.bcf
.. ok

test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G -a -D  /tmp/BaL6TwCRH7/concat.5.a.bcf /tmp/BaL6TwCRH7/concat.5.b.bcf /tmp/BaL6TwCRH7/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -N /builddir/build/BUILD/bcftools-1.23/test/reheader.samples | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -n AAA,BBB | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -s /builddir/build/BUILD/bcftools-1.23/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.23/test/empty.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.23/test/empty.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr /tmp/BaL6TwCRH7/empty.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/empty.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr /tmp/BaL6TwCRH7/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	cat /tmp/BaL6TwCRH7/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /builddir/build/BUILD/bcftools-1.23/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/BaL6TwCRH7/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/BaL6TwCRH7/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /builddir/build/BUILD/bcftools-1.23/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/BaL6TwCRH7/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -h /builddir/build/BUILD/bcftools-1.23/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.23/test/reheader.fai /tmp/BaL6TwCRH7/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.3.fai /builddir/build/BUILD/bcftools-1.23/test/reheader.3.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.3.fai /tmp/BaL6TwCRH7/reheader.3.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.23/bcftools reheader -f /builddir/build/BUILD/bcftools-1.23/test/reheader.3.fai /tmp/BaL6TwCRH7/reheader.3.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/BaL6TwCRH7/rename.map -Ov /tmp/BaL6TwCRH7/annotate.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/BaL6TwCRH7/rename.map -Ob /tmp/BaL6TwCRH7/annotate.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/BaL6TwCRH7/rename.map -Ov /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.23/bcftools annotate --rename-chrs /tmp/BaL6TwCRH7/rename.map -Ob /builddir/build/BUILD/bcftools-1.23/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM\t%POS\n'
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids --3N6 /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids --3N6
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,-
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert  --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert  --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -G /builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.23/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --tag PL /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --tag PL
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --tag PL /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --tag PL
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids /tmp/BaL6TwCRH7/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --vcf-ids /tmp/BaL6TwCRH7/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 /tmp/BaL6TwCRH7/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 /tmp/BaL6TwCRH7/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 --vcf-ids /tmp/BaL6TwCRH7/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g -,. --3N6 --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 --vcf-ids /tmp/BaL6TwCRH7/check.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/check.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -g .,- --3N6 --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -h -,.,. /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h -,.,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. --vcf-ids /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,-,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,.,- /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert -h .,.,-
.. ok

test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -H /builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -H /builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.23/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --haplegendsample -,.,. /tmp/BaL6TwCRH7/convert.hap-missing.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --haplegendsample -,.,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,.
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. --vcf-ids /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample -,. --vcf-ids
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample .,- /tmp/BaL6TwCRH7/convert.vcf.gz
.. ok

test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample .,-
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples | grep -v ^##
.. ok

test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.23/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##
.. ok

test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/convert.gvcf.vcf.gz
.. ok

test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa /tmp/BaL6TwCRH7/convert.gvcf.vcf.gz -Ou | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version
.. ok

test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/BaL6TwCRH7/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.23/test/gvcf.fa | grep -v ^##bcftools
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version  -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.23andme
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -Ou  -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.23andme | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert --no-version  -c -,CHROM,POS,REF,ALT -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.tsv
.. ok

test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.23/bcftools convert -Ou  -c -,CHROM,POS,REF,ALT -f /builddir/build/BUILD/bcftools-1.23/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.23/test/convert.tsv | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.gvcf-missing.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.gvcf-missing.fa --missing N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.gvcf-missing.1.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.gvcf-missing.fa --missing N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.2.fa -s A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.2.fa -s A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s A -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.overlaps.1.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.overlaps.1.fa -s B -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.beyond.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.beyond.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.beyond.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.beyond.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab 
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab -c /tmp/BaL6TwCRH7/consensus.1.chain.new >/dev/null; cat /tmp/BaL6TwCRH7/consensus.1.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab 
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab -c /tmp/BaL6TwCRH7/consensus.2.chain.new >/dev/null; cat /tmp/BaL6TwCRH7/consensus.2.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -I -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -I -s - -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with lc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab --mask-with lc  
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.23/test/consensus.tab -c /tmp/BaL6TwCRH7/consensus.3.chain.new >/dev/null; cat /tmp/BaL6TwCRH7/consensus.3.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1  
.. ok

test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1  -c /tmp/BaL6TwCRH7/consensus.4.chain.new >/dev/null; cat /tmp/BaL6TwCRH7/consensus.4.chain.new
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus2.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus2.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/empty.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?"  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus3.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?"  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?" -p xx_  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus3.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -H 2 -M "?" -p xx_  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus4.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus5.fa --haplotype LA  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus5.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus5.fa --haplotype LA  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus6.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus6.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus6.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 2pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 4pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 1pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus7.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus7.fa -H 3pIu  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP>15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP>15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP<15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus8.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -e 'MinDP<15'  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.9.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.9.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.10.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.1.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.10.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.9.2.fa -H A  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.11.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.11.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.11.fa -s smpl -a N  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.12.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.13.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.13.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.13.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.14.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.14.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.14.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.12.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.12.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.15.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.16.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.16.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H I  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s - -M N -m /builddir/build/BUILD/bcftools-1.23/test/consensus.17.bed 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.17.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus2.fa -s - -M N -m /builddir/build/BUILD/bcftools-1.23/test/consensus.17.bed 
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.18.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.18.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.18.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.19.fa -s -   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.19.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.19.fa -s -   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -s -  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s b  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s b  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s a  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -s a  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.b.txt  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.b.txt  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.a.txt  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.20.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.20.fa -M . -S /builddir/build/BUILD/bcftools-1.23/test/consensus.20.a.txt  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.21.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.21.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.21.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.21.fa   
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2 --mark-del .  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 0  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 1  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2  
.. ok

test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/BaL6TwCRH7/consensus.22.bcf    -f /builddir/build/BUILD/bcftools-1.23/test/consensus.22.fa --regions-overlap 2  
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r 11:10-20 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r 11:10-20 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/iupac.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/BaL6TwCRH7/mpileup.bam.list --no-version | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/BaL6TwCRH7/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/BaL6TwCRH7/mpileup.cram.list --no-version | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/BaL6TwCRH7/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/BaL6TwCRH7/mpileup.bam.list --no-version | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/BaL6TwCRH7/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -b /tmp/BaL6TwCRH7/mpileup.cram.list --no-version | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -r17:100-150 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob -b /tmp/BaL6TwCRH7/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.23/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -S /builddir/build/BUILD/bcftools-1.23/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t17:100-150 -G /builddir/build/BUILD/bcftools-1.23/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s HG00102 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -G /builddir/build/BUILD/bcftools-1.23/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD --indels-cns -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.1.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.fa /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_mpileup:
	/builddir/build/BUILD/bcftools-1.23/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.fa -Ob /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.1.bam /builddir/build/BUILD/bcftools-1.23/test/mpileup/annot-NMBZ.3.2.bam | /builddir/build/BUILD/bcftools-1.23/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.gff3 /builddir/build/BUILD/bcftools-1.23/test/csq.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.chr.gff3 --unify-chr-names -,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.2.gff /builddir/build/BUILD/bcftools-1.23/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.23/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names -,-,- /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names -,-,chr /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names -,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names -,chr,chr /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names chr,chr,chr /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.fa --unify-chr-names chr,-,chr /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names chr,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -g /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.gff -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa --unify-chr-names chr,-,- /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq.nchr.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq.ychr.gff --unify-chr-names Chromosome,chr,- /builddir/build/BUILD/bcftools-1.23/test/csq.yychr.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf  | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf       | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf                 | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000571540/ENST00000571540.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000571540/ENST00000571540.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000571540/nmd.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 0 | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%BCSQ\n' | ../sort-csq -q
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 1 | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%BCSQ\n' | ../sort-csq -q
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000000001 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a -Ot | grep -v ^#
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000000001 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf  | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.23/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENSCAFT00000047742/test.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573035-bt2212/complex-event.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000360372/ENST00000360372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000360372/ENST00000360372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000360372/mnp.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.23/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf  | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q
.. ok

test_csq_real:
	/builddir/build/BUILD/bcftools-1.23/bcftools csq -f /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.23/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.23/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.23/test/roh.1.tab.gz| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.23/test/roh.1.tab.gz --ignore-homref| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^#
.. ok

test_roh:
	/builddir/build/BUILD/bcftools-1.23/bcftools roh /builddir/build/BUILD/bcftools-1.23/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^#
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck --keep-refs /tmp/BaL6TwCRH7/gtcheck.gvcf.a.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck --keep-refs /tmp/BaL6TwCRH7/gtcheck.gvcf.b.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck  /tmp/BaL6TwCRH7/gtcheck.gvcf.a.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck  /tmp/BaL6TwCRH7/gtcheck.gvcf.b.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 --no-HWE-prob /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,GT /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,PL /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,GT /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,PL /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -p s1,s1 /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/BaL6TwCRH7/gtcheck.2.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0  /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.23/test/gtcheck.3.pairs /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 --n-matches 4 /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO  | sort
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -p B,C,B,D /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,GT -H /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u GT,PL -H /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,GT -H /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -u PL,PL -H /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.23/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/BaL6TwCRH7/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.23/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/BaL6TwCRH7/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u GT -e 30 /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u GT -e 300 /tmp/BaL6TwCRH7/gtcheck.1.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -u PL -e 30 /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck  /tmp/BaL6TwCRH7/gtcheck.ntop.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck --n-matches 2 /tmp/BaL6TwCRH7/gtcheck.ntop.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck  /tmp/BaL6TwCRH7/gtcheck.5.vcf.gz -g /tmp/BaL6TwCRH7/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -p A,B,B,C /tmp/BaL6TwCRH7/gtcheck.6.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_gtcheck:
	/builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/BaL6TwCRH7/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/BaL6TwCRH7/merge.4.b.vcf.gz  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/BaL6TwCRH7/merge.4.b.bcf  | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/BaL6TwCRH7/split-vep.2.vcf.gz  -- --hide 'INFO,URL' | grep -v ^##bcftools_
.. ok

test_vcf_plugin:
	export BCFTOOLS_PLUGINS=/builddir/build/BUILD/bcftools-1.23/plugins; /builddir/build/BUILD/bcftools-1.23/bcftools +vcf2table /tmp/BaL6TwCRH7/split-vep.2.bcf  -- --hide 'INFO,URL' | grep -v ^##bcftools_
.. ok


Number of tests:
    total   .. 2396
    passed  .. 2396
    failed  .. 0

+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: bcftools-1.23-1.el10.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.SC2Hje
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.23
+ DOCDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/doc/bcftools
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/doc/bcftools
+ cp -pr /builddir/build/BUILD/bcftools-1.23/AUTHORS /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/doc/bcftools
+ cp -pr /builddir/build/BUILD/bcftools-1.23/NEWS /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/doc/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.8o2TQZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.23
+ LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/licenses/bcftools
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/licenses/bcftools
+ cp -pr /builddir/build/BUILD/bcftools-1.23/LICENSE /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64/usr/share/licenses/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bcftools = 1.23-1.el10 bcftools(aarch-64) = 1.23-1.el10
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl /usr/bin/python3 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(64bit) libhts.so.3(HTSLIB_1.1)(64bit) libhts.so.3(HTSLIB_1.10)(64bit) libhts.so.3(HTSLIB_1.13)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.3)(64bit) libhts.so.3(HTSLIB_1.4)(64bit) libhts.so.3(HTSLIB_1.5)(64bit) libhts.so.3(HTSLIB_1.6)(64bit) libhts.so.3(HTSLIB_1.7)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.40()(64bit) rtld(GNU_HASH)
Conflicts: samtools < 1.0
Processing files: bcftools-debugsource-1.23-1.el10.aarch64
Provides: bcftools-debugsource = 1.23-1.el10 bcftools-debugsource(aarch-64) = 1.23-1.el10
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: bcftools-debuginfo-1.23-1.el10.aarch64
Provides: bcftools-debuginfo = 1.23-1.el10 bcftools-debuginfo(aarch-64) = 1.23-1.el10 debuginfo(build-id) = 01d01e447caa3d27dbe571ddd82fc1ab06137986 debuginfo(build-id) = 03974a692741f8c9d57b99bff64195f37faed8c2 debuginfo(build-id) = 0473e0283566f62339b3394a5763b0866ea797d4 debuginfo(build-id) = 0bad6017fa96156db8c46b03faa48d873d1448b2 debuginfo(build-id) = 0f18a1486ab4a33261d7f72ee1c0faa0849b31df debuginfo(build-id) = 111eda8f23eaf63419799380fb2bcb3b2b741fdc debuginfo(build-id) = 13b89d2a884c2fc7e1113adfdf0393ac2cb96407 debuginfo(build-id) = 15f39682b62d18a68a89b6b864b268f970a67efd debuginfo(build-id) = 17b21f0985e70bec208d31ce9073c2e897fe7f23 debuginfo(build-id) = 18ca6a4f0f17738ef1957770b5ed0f7ec930a6ea debuginfo(build-id) = 18dcd45e95d03eb95f2fa737165c9866f7abf810 debuginfo(build-id) = 248f9279821f48d3fd752c991bcd090cf9c96d72 debuginfo(build-id) = 25f65c5f00e52473d3590d11aef2c1af4f325880 debuginfo(build-id) = 27941edd29e45a550de56c7d6b87270f6adc1d7a debuginfo(build-id) = 30ceca35f20d2991d54bcbca0ef8ae1f9991e8fa debuginfo(build-id) = 3971fb3632209445b1c8e0390d72e9432f42d8fd debuginfo(build-id) = 4292d1a0f607461e4579017c2c56f6ff1054b297 debuginfo(build-id) = 464271f532dc9ce8eb79c7a2a629cc0241738eb0 debuginfo(build-id) = 48db7e7eb4235bd3e158fa3290e79f73a5deccf9 debuginfo(build-id) = 4909b975acb14f551f5348f75e5fe2ebbf7c766c debuginfo(build-id) = 59fc556166281600f23efdcaf9c57759dcf8ec13 debuginfo(build-id) = 62900779a6be7d84c39b8fed7851e2edc0937e59 debuginfo(build-id) = 6a4bfff97067ec854fb9147285f213885a9ff1aa debuginfo(build-id) = 70d1731baf89b02ccfaa9049cdc3dcfceac949ec debuginfo(build-id) = 70d96a46ff286db2daac2b4a2a882190f8e8a031 debuginfo(build-id) = 760c571c3b99c76d181f0fdaf70ca247b692f578 debuginfo(build-id) = 796222d7dcd62067471b84cceb953041992a4190 debuginfo(build-id) = 7dac9764e7bde4b773ca6af3ce6b4318752777fd debuginfo(build-id) = 84e750197f30d658bdd037eb2723fd2604ad6d12 debuginfo(build-id) = aecbd2c62329b41e26c547d9e687977fb51190b8 debuginfo(build-id) = b1ed9d77c4e3367fe7e4745539f80c5e4c14096c debuginfo(build-id) = b7b262df09bb9942bc944c8d9cb03e0acb71152e debuginfo(build-id) = c41812b07313f4c72108f2a24fbd8710b3de3097 debuginfo(build-id) = c805371513d12f64c54056f85687904059d1251e debuginfo(build-id) = cb5a963ccfbc72274160d5d0cc92e2289c08cc47 debuginfo(build-id) = cb9af2fda3cca87b3559497ff1d03ed4fc199764 debuginfo(build-id) = dcca820ca1840e2d5a6f32f3030b35509d54143b debuginfo(build-id) = deb01046eb951b690d5d00016d622cc4bc0d3ca1 debuginfo(build-id) = eb0759d95b2afc8454c7a09fff0c5958dedb490a debuginfo(build-id) = eb7cea004f841ca2ecc5e07e75b63dc88c53afc5 debuginfo(build-id) = f58c5f6afcbdc6c207bf8ebda869aee4a7477a43 debuginfo(build-id) = fb45f14fbdae6a75f9231d7d9fe1e7140928723d
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: bcftools-debugsource(aarch-64) = 1.23-1.el10
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64
Wrote: /builddir/build/RPMS/bcftools-1.23-1.el10.aarch64.rpm
Wrote: /builddir/build/RPMS/bcftools-debugsource-1.23-1.el10.aarch64.rpm
Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.23-1.el10.aarch64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.xyIsnh
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.23
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.23-1.el10.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.xsakVw
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/bcftools-1.23-SPECPARTS
+ rm -rf bcftools-1.23 bcftools-1.23.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild bcftools-1.23-1.el10.src.rpm
Finish: build phase for bcftools-1.23-1.el10.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root/var/log/dnf.rpm.log
/var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root/var/log/dnf.librepo.log
/var/lib/mock/centos-stream+epel-10-aarch64-1769502044.615196/root/var/log/dnf.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
INFO: Done(/var/lib/copr-rpmbuild/results/bcftools-1.23-1.el10.src.rpm) Config(child) 1 minutes 33 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "bcftools-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.el10",
            "arch": "aarch64"
        },
        {
            "name": "bcftools-debugsource",
            "epoch": null,
            "version": "1.23",
            "release": "1.el10",
            "arch": "aarch64"
        },
        {
            "name": "bcftools",
            "epoch": null,
            "version": "1.23",
            "release": "1.el10",
            "arch": "aarch64"
        },
        {
            "name": "bcftools",
            "epoch": null,
            "version": "1.23",
            "release": "1.el10",
            "arch": "src"
        }
    ]
}
RPMResults finished