Warning: Permanently added '13.221.177.235' (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/10066873-epel-10-x86_64 --chroot epel-10-x86_64 Version: 1.6 PID: 41068 Logging PID: 41070 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 10066873, 'buildroot_pkgs': [], 'chroot': 'epel-10-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'e14e663825689d893c3d0d37656f4dd10cee491c', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/bcftools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bcftools', 'package_version': '1.23-1', 'project_dirname': 'staging', 'project_name': 'staging', 'project_owner': 'ron', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/staging/epel-10-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ron/staging--ron', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'ron', 'tags': [], 'task_id': '10066873-epel-10-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/staging/bcftools /var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/bcftools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/bcftools', '/var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/bcftools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/bcftools'... Running: git checkout e14e663825689d893c3d0d37656f4dd10cee491c -- cmd: ['git', 'checkout', 'e14e663825689d893c3d0d37656f4dd10cee491c', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/bcftools rc: 0 stdout: stderr: Note: switching to 'e14e663825689d893c3d0d37656f4dd10cee491c'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at e14e663 automatic import of bcftools Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/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/staging/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 332M 0 --:--:-- --:--:-- --:--:-- 337M 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-p7qk1sbd/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509085.666809 -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-p7qk1sbd/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-p7qk1sbd/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769509085.666809 -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-p7qk1sbd/bcftools/bcftools.spec) Config(centos-stream+epel-10-x86_64) 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-x86_64-bootstrap-1769509085.666809/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-1e6061aa-e4b3-4850-8348-be268556966c INFO: Checking that eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e image matches host's architecture INFO: Copy content of container eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e to /var/lib/mock/centos-stream+epel-10-x86_64-bootstrap-1769509085.666809/root INFO: mounting eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e with podman image mount INFO: image eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e as /var/lib/containers/storage/overlay/8872e0cb5314b16ee0111ed12766e11e60dd706010199a1dbc0f2046bf1eb964/merged INFO: umounting image eee3feca625505a534e2f5b3e36aae2f6c3e3e929f8b5a4701e335a06a83735e (/var/lib/containers/storage/overlay/8872e0cb5314b16ee0111ed12766e11e60dd706010199a1dbc0f2046bf1eb964/merged) with podman image umount INFO: Removing image mock-bootstrap-1e6061aa-e4b3-4850-8348-be268556966c 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-x86_64-1769509085.666809/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.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 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 50 kB/s | 3.5 kB 00:00 CentOS Stream 10 - BaseOS 26 MB/s | 6.9 MB 00:00 CentOS Stream 10 - AppStream 15 MB/s | 3.5 MB 00:00 CentOS Stream 10 - CRB 3.7 MB/s | 795 kB 00:00 CentOS Stream 10 - Extras packages 37 kB/s | 8.3 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 20 MB/s | 6.2 MB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: bash x86_64 5.2.26-6.el10 baseos 1.8 M bzip2 x86_64 1.0.8-25.el10 baseos 54 k centos-stream-release noarch 10.0-19.el10 baseos 30 k coreutils x86_64 9.5-6.el10 baseos 1.1 M cpio x86_64 2.15-3.el10 baseos 292 k diffutils x86_64 3.10-8.el10 baseos 409 k epel-rpm-macros noarch 10-6.el10_2 epel 8.2 k findutils x86_64 1:4.10.0-5.el10 baseos 551 k gawk x86_64 5.3.0-6.el10 baseos 1.1 M glibc-minimal-langpack x86_64 2.39-99.el10 baseos 39 k grep x86_64 3.11-10.el10 baseos 301 k gzip x86_64 1.13-3.el10 baseos 170 k info x86_64 7.1-6.el10 baseos 183 k patch x86_64 2.7.6-26.el10 appstream 132 k redhat-rpm-config noarch 295-1.el10 appstream 74 k rpm-build x86_64 4.19.1.1-21.el10 appstream 75 k sed x86_64 4.9-3.el10 baseos 318 k shadow-utils x86_64 2:4.15.0-9.el10 baseos 1.3 M tar x86_64 2:1.35-10.el10 baseos 864 k unzip x86_64 6.0-69.el10 baseos 190 k util-linux x86_64 2.40.2-13.el10 baseos 1.3 M which x86_64 2.21-44.el10 baseos 42 k xz x86_64 1:5.6.2-4.el10 baseos 481 k Installing dependencies: alternatives x86_64 1.30-2.el10 baseos 42 k ansible-srpm-macros noarch 1-16.1.el10_0 epel 20 k audit-libs x86_64 4.0.3-5.el10 baseos 131 k authselect x86_64 1.5.0-8.el10 baseos 144 k authselect-libs x86_64 1.5.0-8.el10 baseos 223 k basesystem noarch 11-22.el10 baseos 4.3 k binutils x86_64 2.41-60.el10 baseos 6.4 M binutils-gold x86_64 2.41-60.el10 baseos 797 k bzip2-libs x86_64 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 x86_64 9.5-6.el10 baseos 2.1 M cracklib x86_64 2.9.11-8.el10 baseos 96 k cracklib-dicts x86_64 2.9.11-8.el10 baseos 3.6 M crypto-policies noarch 20251127-1.git27c2902.el10 baseos 98 k curl x86_64 8.12.1-4.el10 baseos 217 k cyrus-sasl-lib x86_64 2.1.28-27.el10 baseos 106 k debugedit x86_64 5.1-8.el10 appstream 80 k dwz x86_64 0.16-1.el10 appstream 140 k ed x86_64 1.20-5.el10 baseos 83 k efi-srpm-macros noarch 6-6.el10 appstream 24 k elfutils x86_64 0.194-1.el10 baseos 573 k elfutils-debuginfod-client x86_64 0.194-1.el10 baseos 43 k elfutils-default-yama-scope noarch 0.194-1.el10 baseos 8.3 k elfutils-libelf x86_64 0.194-1.el10 baseos 201 k elfutils-libs x86_64 0.194-1.el10 baseos 267 k file x86_64 5.45-8.el10 baseos 49 k file-libs x86_64 5.45-8.el10 baseos 764 k filesystem x86_64 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 x86_64 16.3-2.el10 appstream 4.4 M gdbm x86_64 1:1.23-14.el10 baseos 151 k gdbm-libs x86_64 1:1.23-14.el10 baseos 57 k ghc-srpm-macros noarch 1.9.2-1.el10_0 epel 9.1 k glibc x86_64 2.39-99.el10 baseos 2.1 M glibc-common x86_64 2.39-99.el10 baseos 333 k glibc-gconv-extra x86_64 2.39-99.el10 baseos 1.7 M gmp x86_64 1:6.2.1-12.el10 baseos 318 k go-srpm-macros noarch 3.8.0-1.el10 appstream 27 k jansson x86_64 2.14-3.el10 baseos 46 k json-c x86_64 0.18-3.el10 baseos 45 k kernel-srpm-macros noarch 1.0-27.el10 appstream 8.7 k keyutils-libs x86_64 1.6.3-5.el10 baseos 33 k krb5-libs x86_64 1.21.3-8.el10 baseos 767 k libacl x86_64 2.3.2-4.el10 baseos 25 k libarchive x86_64 3.7.7-4.el10 baseos 414 k libattr x86_64 2.5.2-5.el10 baseos 19 k libblkid x86_64 2.40.2-13.el10 baseos 124 k libbrotli x86_64 1.1.0-7.el10 baseos 344 k libcap x86_64 2.69-7.el10 baseos 91 k libcap-ng x86_64 0.8.4-6.el10 baseos 33 k libcom_err x86_64 1.47.1-5.el10 baseos 26 k libcurl x86_64 8.12.1-4.el10 baseos 368 k libeconf x86_64 0.6.2-4.el10 baseos 33 k libevent x86_64 2.1.12-16.el10 baseos 261 k libfdisk x86_64 2.40.2-13.el10 baseos 159 k libffi x86_64 3.4.4-10.el10 baseos 41 k libgcc x86_64 14.3.1-4.2.el10 baseos 147 k libgomp x86_64 14.3.1-4.2.el10 baseos 370 k libidn2 x86_64 2.3.7-3.el10 baseos 118 k libmount x86_64 2.40.2-13.el10 baseos 155 k libnghttp2 x86_64 1.64.0-2.el10 baseos 78 k libpkgconf x86_64 2.1.0-3.el10 baseos 39 k libpsl x86_64 0.21.5-6.el10 baseos 65 k libpwquality x86_64 1.4.5-12.el10 baseos 123 k libselinux x86_64 3.9-3.el10 baseos 97 k libsemanage x86_64 3.9-2.el10 baseos 121 k libsepol x86_64 3.9-1.el10 baseos 348 k libsmartcols x86_64 2.40.2-13.el10 baseos 83 k libssh x86_64 0.11.1-3.el10 baseos 233 k libssh-config noarch 0.11.1-3.el10 baseos 8.4 k libstdc++ x86_64 14.3.1-4.2.el10 baseos 926 k libtasn1 x86_64 4.20.0-1.el10 baseos 75 k libunistring x86_64 1.1-10.el10 baseos 548 k libutempter x86_64 1.2.1-15.el10 baseos 27 k libuuid x86_64 2.40.2-13.el10 baseos 28 k libverto x86_64 0.3.2-10.el10 baseos 22 k libxcrypt x86_64 4.4.36-10.el10 baseos 120 k libxml2 x86_64 2.12.5-9.el10 baseos 692 k libzstd x86_64 1.5.5-9.el10 baseos 292 k lua-libs x86_64 5.4.6-7.el10 baseos 132 k lua-srpm-macros noarch 1-15.el10 appstream 9.8 k lz4-libs x86_64 1.9.4-8.el10 baseos 68 k mpfr x86_64 4.2.1-6.el10 baseos 346 k ncurses-base noarch 6.4-14.20240127.el10 baseos 100 k ncurses-libs x86_64 6.4-14.20240127.el10 baseos 338 k ocaml-srpm-macros noarch 10-4.el10 appstream 10 k openblas-srpm-macros noarch 2-19.el10 appstream 8.7 k openldap x86_64 2.6.10-1.el10 baseos 239 k openssl-fips-provider x86_64 1:3.5.1-6.el10 baseos 812 k openssl-libs x86_64 1:3.5.1-6.el10 baseos 2.3 M p11-kit x86_64 0.26.1-1.el10 baseos 559 k p11-kit-trust x86_64 0.26.1-1.el10 baseos 141 k package-notes-srpm-macros noarch 0.5-13.el10 appstream 10 k pam x86_64 1.6.1-9.el10 baseos 584 k pam-libs x86_64 1.6.1-9.el10 baseos 56 k pcre2 x86_64 10.44-1.el10.3 baseos 248 k pcre2-syntax noarch 10.44-1.el10.3 baseos 151 k perl-srpm-macros noarch 1-57.el10 appstream 9.5 k pkgconf x86_64 2.1.0-3.el10 baseos 45 k pkgconf-m4 noarch 2.1.0-3.el10 baseos 15 k pkgconf-pkg-config x86_64 2.1.0-3.el10 baseos 11 k popt x86_64 1.19-8.el10 baseos 66 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 x86_64 8.2-11.el10 baseos 214 k rpm x86_64 4.19.1.1-21.el10 baseos 560 k rpm-build-libs x86_64 4.19.1.1-21.el10 baseos 92 k rpm-libs x86_64 4.19.1.1-21.el10 baseos 309 k rpm-sequoia x86_64 1.9.0.3-1.el10 baseos 975 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 x86_64 3.46.1-5.el10 baseos 745 k systemd-libs x86_64 257-21.el10 baseos 828 k util-linux-core x86_64 2.40.2-13.el10 baseos 550 k xz-libs x86_64 1:5.6.2-4.el10 baseos 113 k zip x86_64 3.0-45.el10 baseos 270 k zlib-ng-compat x86_64 2.2.3-3.el10 baseos 76 k zstd x86_64 1.5.5-9.el10 baseos 464 k Transaction Summary ================================================================================ Install 147 Packages Total download size: 61 M Installed size: 188 M Downloading Packages: (1/147): alternatives-1.30-2.el10.x86_64.rpm 3.9 MB/s | 42 kB 00:00 (2/147): audit-libs-4.0.3-5.el10.x86_64.rpm 9.5 MB/s | 131 kB 00:00 (3/147): authselect-libs-1.5.0-8.el10.x86_64.rp 60 MB/s | 223 kB 00:00 (4/147): basesystem-11-22.el10.noarch.rpm 2.3 MB/s | 4.3 kB 00:00 (5/147): authselect-1.5.0-8.el10.x86_64.rpm 8.7 MB/s | 144 kB 00:00 (6/147): bash-5.2.26-6.el10.x86_64.rpm 231 MB/s | 1.8 MB 00:00 (7/147): binutils-gold-2.41-60.el10.x86_64.rpm 63 MB/s | 797 kB 00:00 (8/147): bzip2-1.0.8-25.el10.x86_64.rpm 7.0 MB/s | 54 kB 00:00 (9/147): binutils-2.41-60.el10.x86_64.rpm 276 MB/s | 6.4 MB 00:00 (10/147): bzip2-libs-1.0.8-25.el10.x86_64.rpm 4.0 MB/s | 42 kB 00:00 (11/147): ca-certificates-2025.2.80_v9.0.305-10 92 MB/s | 1.1 MB 00:00 (12/147): centos-gpg-keys-10.0-19.el10.noarch.r 6.3 MB/s | 26 kB 00:00 (13/147): centos-stream-release-10.0-19.el10.no 7.2 MB/s | 30 kB 00:00 (14/147): centos-stream-repos-10.0-19.el10.noar 8.3 MB/s | 12 kB 00:00 (15/147): coreutils-9.5-6.el10.x86_64.rpm 214 MB/s | 1.1 MB 00:00 (16/147): cpio-2.15-3.el10.x86_64.rpm 44 MB/s | 292 kB 00:00 (17/147): coreutils-common-9.5-6.el10.x86_64.rp 210 MB/s | 2.1 MB 00:00 (18/147): cracklib-2.9.11-8.el10.x86_64.rpm 17 MB/s | 96 kB 00:00 (19/147): cracklib-dicts-2.9.11-8.el10.x86_64.r 291 MB/s | 3.6 MB 00:00 (20/147): crypto-policies-20251127-1.git27c2902 9.7 MB/s | 98 kB 00:00 (21/147): curl-8.12.1-4.el10.x86_64.rpm 21 MB/s | 217 kB 00:00 (22/147): cyrus-sasl-lib-2.1.28-27.el10.x86_64. 44 MB/s | 106 kB 00:00 (23/147): diffutils-3.10-8.el10.x86_64.rpm 115 MB/s | 409 kB 00:00 (24/147): ed-1.20-5.el10.x86_64.rpm 23 MB/s | 83 kB 00:00 (25/147): elfutils-0.194-1.el10.x86_64.rpm 158 MB/s | 573 kB 00:00 (26/147): elfutils-debuginfod-client-0.194-1.el 18 MB/s | 43 kB 00:00 (27/147): elfutils-default-yama-scope-0.194-1.e 4.0 MB/s | 8.3 kB 00:00 (28/147): file-5.45-8.el10.x86_64.rpm 34 MB/s | 49 kB 00:00 (29/147): elfutils-libelf-0.194-1.el10.x86_64.r 74 MB/s | 201 kB 00:00 (30/147): elfutils-libs-0.194-1.el10.x86_64.rpm 83 MB/s | 267 kB 00:00 (31/147): file-libs-5.45-8.el10.x86_64.rpm 177 MB/s | 764 kB 00:00 (32/147): findutils-4.10.0-5.el10.x86_64.rpm 77 MB/s | 551 kB 00:00 (33/147): filesystem-3.18-17.el10.x86_64.rpm 277 MB/s | 4.8 MB 00:00 (34/147): gawk-5.3.0-6.el10.x86_64.rpm 68 MB/s | 1.1 MB 00:00 (35/147): gdbm-1.23-14.el10.x86_64.rpm 12 MB/s | 151 kB 00:00 (36/147): gdbm-libs-1.23-14.el10.x86_64.rpm 20 MB/s | 57 kB 00:00 (37/147): glibc-2.39-99.el10.x86_64.rpm 302 MB/s | 2.1 MB 00:00 (38/147): glibc-common-2.39-99.el10.x86_64.rpm 44 MB/s | 333 kB 00:00 (39/147): glibc-gconv-extra-2.39-99.el10.x86_64 161 MB/s | 1.7 MB 00:00 (40/147): glibc-minimal-langpack-2.39-99.el10.x 9.1 MB/s | 39 kB 00:00 (41/147): gmp-6.2.1-12.el10.x86_64.rpm 66 MB/s | 318 kB 00:00 (42/147): grep-3.11-10.el10.x86_64.rpm 83 MB/s | 301 kB 00:00 (43/147): gzip-1.13-3.el10.x86_64.rpm 43 MB/s | 170 kB 00:00 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kB 00:00 (147/147): ghc-srpm-macros-1.9.2-1.el10_0.noarc 3.0 MB/s | 9.1 kB 00:00 -------------------------------------------------------------------------------- Total 54 MB/s | 61 MB 00:01 CentOS Stream 10 - BaseOS 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x8483C65D: Userid : "CentOS (CentOS Official Signing Key) " 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 - x86_64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xE37ED158: Userid : "Fedora (epel10) " 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.x86_64 1/1 Preparing : 1/1 Installing : libgcc-14.3.1-4.2.el10.x86_64 1/147 Running scriptlet: libgcc-14.3.1-4.2.el10.x86_64 1/147 Installing : ghc-srpm-macros-1.9.2-1.el10_0.noarch 2/147 Installing : fpc-srpm-macros-1.3-7.el10_1.noarch 3/147 Installing : ansible-srpm-macros-1-16.1.el10_0.noarch 4/147 Installing : rust-toolset-srpm-macros-1.92.0-1.el10.noarch 5/147 Installing : qt6-srpm-macros-6.10.1-1.el10.noarch 6/147 Installing : perl-srpm-macros-1-57.el10.noarch 7/147 Installing : package-notes-srpm-macros-0.5-13.el10.noarch 8/147 Installing : openblas-srpm-macros-2-19.el10.noarch 9/147 Installing : ocaml-srpm-macros-10-4.el10.noarch 10/147 Installing : kernel-srpm-macros-1.0-27.el10.noarch 11/147 Installing : publicsuffix-list-dafsa-20240107-5.el10.noarch 12/147 Installing : pkgconf-m4-2.1.0-3.el10.noarch 13/147 Installing : pcre2-syntax-10.44-1.el10.3.noarch 14/147 Installing : ncurses-base-6.4-14.20240127.el10.noarch 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p11-kit-trust-0.26.1-1.el10.x86_64 83/147 Running scriptlet: p11-kit-trust-0.26.1-1.el10.x86_64 83/147 Installing : openssl-fips-provider-1:3.5.1-6.el10.x86_64 84/147 Installing : openssl-libs-1:3.5.1-6.el10.x86_64 85/147 Installing : coreutils-9.5-6.el10.x86_64 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.x86_64 88/147 Installing : gzip-1.13-3.el10.x86_64 89/147 Installing : cracklib-2.9.11-8.el10.x86_64 90/147 Installing : cracklib-dicts-2.9.11-8.el10.x86_64 91/147 Installing : libpwquality-1.4.5-12.el10.x86_64 92/147 Installing : libevent-2.1.12-16.el10.x86_64 93/147 Installing : rpm-sequoia-1.9.0.3-1.el10.x86_64 94/147 Installing : zip-3.0-45.el10.x86_64 95/147 Installing : cyrus-sasl-lib-2.1.28-27.el10.x86_64 96/147 Installing : openldap-2.6.10-1.el10.x86_64 97/147 Installing : gdbm-1:1.23-14.el10.x86_64 98/147 Installing : pam-1.6.1-9.el10.x86_64 99/147 Installing : libfdisk-2.40.2-13.el10.x86_64 100/147 Installing : libxml2-2.12.5-9.el10.x86_64 101/147 Installing : libarchive-3.7.7-4.el10.x86_64 102/147 Installing : bzip2-1.0.8-25.el10.x86_64 103/147 Installing : sqlite-libs-3.46.1-5.el10.x86_64 104/147 Installing : rpm-libs-4.19.1.1-21.el10.x86_64 105/147 Installing : ed-1.20-5.el10.x86_64 106/147 Installing : patch-2.7.6-26.el10.x86_64 107/147 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.x86_64 109/147 Installing : diffutils-3.10-8.el10.x86_64 110/147 Installing : json-c-0.18-3.el10.x86_64 111/147 Installing : keyutils-libs-1.6.3-5.el10.x86_64 112/147 Installing : libbrotli-1.1.0-7.el10.x86_64 113/147 Installing : libcom_err-1.47.1-5.el10.x86_64 114/147 Installing : libgomp-14.3.1-4.2.el10.x86_64 115/147 Installing : libnghttp2-1.64.0-2.el10.x86_64 116/147 Installing : libpkgconf-2.1.0-3.el10.x86_64 117/147 Installing : pkgconf-2.1.0-3.el10.x86_64 118/147 Installing : pkgconf-pkg-config-2.1.0-3.el10.x86_64 119/147 Installing : libverto-0.3.2-10.el10.x86_64 120/147 Installing : krb5-libs-1.21.3-8.el10.x86_64 121/147 Installing : libssh-0.11.1-3.el10.x86_64 122/147 Installing : libcurl-8.12.1-4.el10.x86_64 123/147 Installing : elfutils-libs-0.194-1.el10.x86_64 124/147 Installing : elfutils-debuginfod-client-0.194-1.el10.x86_64 125/147 Installing : binutils-gold-2.41-60.el10.x86_64 126/147 Running scriptlet: binutils-gold-2.41-60.el10.x86_64 126/147 Installing : binutils-2.41-60.el10.x86_64 127/147 Running scriptlet: binutils-2.41-60.el10.x86_64 127/147 Installing : elfutils-0.194-1.el10.x86_64 128/147 Installing : gdb-minimal-16.3-2.el10.x86_64 129/147 Installing : debugedit-5.1-8.el10.x86_64 130/147 Installing : rpm-build-libs-4.19.1.1-21.el10.x86_64 131/147 Installing : curl-8.12.1-4.el10.x86_64 132/147 Running scriptlet: rpm-4.19.1.1-21.el10.x86_64 133/147 Installing : rpm-4.19.1.1-21.el10.x86_64 133/147 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.x86_64 141/147 Installing : pyproject-srpm-macros-1.18.5-1.el10.noarch 142/147 Installing : util-linux-2.40.2-13.el10.x86_64 143/147 Running scriptlet: util-linux-2.40.2-13.el10.x86_64 143/147 Installing : authselect-1.5.0-8.el10.x86_64 144/147 Installing : which-2.21-44.el10.x86_64 145/147 Installing : info-7.1-6.el10.x86_64 146/147 Installing : epel-rpm-macros-10-6.el10_2.noarch 147/147 Running scriptlet: filesystem-3.18-17.el10.x86_64 147/147 Running scriptlet: ca-certificates-2025.2.80_v9.0.305-102.el10.noar 147/147 Running scriptlet: authselect-libs-1.5.0-8.el10.x86_64 147/147 Running scriptlet: rpm-4.19.1.1-21.el10.x86_64 147/147 Running scriptlet: epel-rpm-macros-10-6.el10_2.noarch 147/147 Installed: alternatives-1.30-2.el10.x86_64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.x86_64 authselect-1.5.0-8.el10.x86_64 authselect-libs-1.5.0-8.el10.x86_64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.x86_64 binutils-2.41-60.el10.x86_64 binutils-gold-2.41-60.el10.x86_64 bzip2-1.0.8-25.el10.x86_64 bzip2-libs-1.0.8-25.el10.x86_64 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.x86_64 coreutils-common-9.5-6.el10.x86_64 cpio-2.15-3.el10.x86_64 cracklib-2.9.11-8.el10.x86_64 cracklib-dicts-2.9.11-8.el10.x86_64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.x86_64 cyrus-sasl-lib-2.1.28-27.el10.x86_64 debugedit-5.1-8.el10.x86_64 diffutils-3.10-8.el10.x86_64 dwz-0.16-1.el10.x86_64 ed-1.20-5.el10.x86_64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.x86_64 elfutils-debuginfod-client-0.194-1.el10.x86_64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.x86_64 elfutils-libs-0.194-1.el10.x86_64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.x86_64 file-libs-5.45-8.el10.x86_64 filesystem-3.18-17.el10.x86_64 findutils-1:4.10.0-5.el10.x86_64 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.x86_64 gdb-minimal-16.3-2.el10.x86_64 gdbm-1:1.23-14.el10.x86_64 gdbm-libs-1:1.23-14.el10.x86_64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.x86_64 glibc-common-2.39-99.el10.x86_64 glibc-gconv-extra-2.39-99.el10.x86_64 glibc-minimal-langpack-2.39-99.el10.x86_64 gmp-1:6.2.1-12.el10.x86_64 go-srpm-macros-3.8.0-1.el10.noarch grep-3.11-10.el10.x86_64 gzip-1.13-3.el10.x86_64 info-7.1-6.el10.x86_64 jansson-2.14-3.el10.x86_64 json-c-0.18-3.el10.x86_64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.x86_64 krb5-libs-1.21.3-8.el10.x86_64 libacl-2.3.2-4.el10.x86_64 libarchive-3.7.7-4.el10.x86_64 libattr-2.5.2-5.el10.x86_64 libblkid-2.40.2-13.el10.x86_64 libbrotli-1.1.0-7.el10.x86_64 libcap-2.69-7.el10.x86_64 libcap-ng-0.8.4-6.el10.x86_64 libcom_err-1.47.1-5.el10.x86_64 libcurl-8.12.1-4.el10.x86_64 libeconf-0.6.2-4.el10.x86_64 libevent-2.1.12-16.el10.x86_64 libfdisk-2.40.2-13.el10.x86_64 libffi-3.4.4-10.el10.x86_64 libgcc-14.3.1-4.2.el10.x86_64 libgomp-14.3.1-4.2.el10.x86_64 libidn2-2.3.7-3.el10.x86_64 libmount-2.40.2-13.el10.x86_64 libnghttp2-1.64.0-2.el10.x86_64 libpkgconf-2.1.0-3.el10.x86_64 libpsl-0.21.5-6.el10.x86_64 libpwquality-1.4.5-12.el10.x86_64 libselinux-3.9-3.el10.x86_64 libsemanage-3.9-2.el10.x86_64 libsepol-3.9-1.el10.x86_64 libsmartcols-2.40.2-13.el10.x86_64 libssh-0.11.1-3.el10.x86_64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.x86_64 libtasn1-4.20.0-1.el10.x86_64 libunistring-1.1-10.el10.x86_64 libutempter-1.2.1-15.el10.x86_64 libuuid-2.40.2-13.el10.x86_64 libverto-0.3.2-10.el10.x86_64 libxcrypt-4.4.36-10.el10.x86_64 libxml2-2.12.5-9.el10.x86_64 libzstd-1.5.5-9.el10.x86_64 lua-libs-5.4.6-7.el10.x86_64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.x86_64 mpfr-4.2.1-6.el10.x86_64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.x86_64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.x86_64 openssl-fips-provider-1:3.5.1-6.el10.x86_64 openssl-libs-1:3.5.1-6.el10.x86_64 p11-kit-0.26.1-1.el10.x86_64 p11-kit-trust-0.26.1-1.el10.x86_64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.x86_64 pam-libs-1.6.1-9.el10.x86_64 patch-2.7.6-26.el10.x86_64 pcre2-10.44-1.el10.3.x86_64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.x86_64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.x86_64 popt-1.19-8.el10.x86_64 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.x86_64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.x86_64 rpm-build-4.19.1.1-21.el10.x86_64 rpm-build-libs-4.19.1.1-21.el10.x86_64 rpm-libs-4.19.1.1-21.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.x86_64 setup-2.14.5-7.el10.noarch shadow-utils-2:4.15.0-9.el10.x86_64 sqlite-libs-3.46.1-5.el10.x86_64 systemd-libs-257-21.el10.x86_64 tar-2:1.35-10.el10.x86_64 unzip-6.0-69.el10.x86_64 util-linux-2.40.2-13.el10.x86_64 util-linux-core-2.40.2-13.el10.x86_64 which-2.21-44.el10.x86_64 xz-1:5.6.2-4.el10.x86_64 xz-libs-1:5.6.2-4.el10.x86_64 zip-3.0-45.el10.x86_64 zlib-ng-compat-2.2.3-3.el10.x86_64 zstd-1.5.5-9.el10.x86_64 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.x86_64 ansible-srpm-macros-1-16.1.el10_0.noarch audit-libs-4.0.3-5.el10.x86_64 authselect-1.5.0-8.el10.x86_64 authselect-libs-1.5.0-8.el10.x86_64 basesystem-11-22.el10.noarch bash-5.2.26-6.el10.x86_64 binutils-2.41-60.el10.x86_64 binutils-gold-2.41-60.el10.x86_64 bzip2-1.0.8-25.el10.x86_64 bzip2-libs-1.0.8-25.el10.x86_64 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.x86_64 coreutils-common-9.5-6.el10.x86_64 cpio-2.15-3.el10.x86_64 cracklib-2.9.11-8.el10.x86_64 cracklib-dicts-2.9.11-8.el10.x86_64 crypto-policies-20251127-1.git27c2902.el10.noarch curl-8.12.1-4.el10.x86_64 cyrus-sasl-lib-2.1.28-27.el10.x86_64 debugedit-5.1-8.el10.x86_64 diffutils-3.10-8.el10.x86_64 dwz-0.16-1.el10.x86_64 ed-1.20-5.el10.x86_64 efi-srpm-macros-6-6.el10.noarch elfutils-0.194-1.el10.x86_64 elfutils-debuginfod-client-0.194-1.el10.x86_64 elfutils-default-yama-scope-0.194-1.el10.noarch elfutils-libelf-0.194-1.el10.x86_64 elfutils-libs-0.194-1.el10.x86_64 epel-rpm-macros-10-6.el10_2.noarch file-5.45-8.el10.x86_64 file-libs-5.45-8.el10.x86_64 filesystem-3.18-17.el10.x86_64 findutils-4.10.0-5.el10.x86_64 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.x86_64 gdb-minimal-16.3-2.el10.x86_64 gdbm-1.23-14.el10.x86_64 gdbm-libs-1.23-14.el10.x86_64 ghc-srpm-macros-1.9.2-1.el10_0.noarch glibc-2.39-99.el10.x86_64 glibc-common-2.39-99.el10.x86_64 glibc-gconv-extra-2.39-99.el10.x86_64 glibc-minimal-langpack-2.39-99.el10.x86_64 gmp-6.2.1-12.el10.x86_64 go-srpm-macros-3.8.0-1.el10.noarch gpg-pubkey-8483c65d-5ccc5b19 gpg-pubkey-e37ed158-65785fa9 grep-3.11-10.el10.x86_64 gzip-1.13-3.el10.x86_64 info-7.1-6.el10.x86_64 jansson-2.14-3.el10.x86_64 json-c-0.18-3.el10.x86_64 kernel-srpm-macros-1.0-27.el10.noarch keyutils-libs-1.6.3-5.el10.x86_64 krb5-libs-1.21.3-8.el10.x86_64 libacl-2.3.2-4.el10.x86_64 libarchive-3.7.7-4.el10.x86_64 libattr-2.5.2-5.el10.x86_64 libblkid-2.40.2-13.el10.x86_64 libbrotli-1.1.0-7.el10.x86_64 libcap-2.69-7.el10.x86_64 libcap-ng-0.8.4-6.el10.x86_64 libcom_err-1.47.1-5.el10.x86_64 libcurl-8.12.1-4.el10.x86_64 libeconf-0.6.2-4.el10.x86_64 libevent-2.1.12-16.el10.x86_64 libfdisk-2.40.2-13.el10.x86_64 libffi-3.4.4-10.el10.x86_64 libgcc-14.3.1-4.2.el10.x86_64 libgomp-14.3.1-4.2.el10.x86_64 libidn2-2.3.7-3.el10.x86_64 libmount-2.40.2-13.el10.x86_64 libnghttp2-1.64.0-2.el10.x86_64 libpkgconf-2.1.0-3.el10.x86_64 libpsl-0.21.5-6.el10.x86_64 libpwquality-1.4.5-12.el10.x86_64 libselinux-3.9-3.el10.x86_64 libsemanage-3.9-2.el10.x86_64 libsepol-3.9-1.el10.x86_64 libsmartcols-2.40.2-13.el10.x86_64 libssh-0.11.1-3.el10.x86_64 libssh-config-0.11.1-3.el10.noarch libstdc++-14.3.1-4.2.el10.x86_64 libtasn1-4.20.0-1.el10.x86_64 libunistring-1.1-10.el10.x86_64 libutempter-1.2.1-15.el10.x86_64 libuuid-2.40.2-13.el10.x86_64 libverto-0.3.2-10.el10.x86_64 libxcrypt-4.4.36-10.el10.x86_64 libxml2-2.12.5-9.el10.x86_64 libzstd-1.5.5-9.el10.x86_64 lua-libs-5.4.6-7.el10.x86_64 lua-srpm-macros-1-15.el10.noarch lz4-libs-1.9.4-8.el10.x86_64 mpfr-4.2.1-6.el10.x86_64 ncurses-base-6.4-14.20240127.el10.noarch ncurses-libs-6.4-14.20240127.el10.x86_64 ocaml-srpm-macros-10-4.el10.noarch openblas-srpm-macros-2-19.el10.noarch openldap-2.6.10-1.el10.x86_64 openssl-fips-provider-3.5.1-6.el10.x86_64 openssl-libs-3.5.1-6.el10.x86_64 p11-kit-0.26.1-1.el10.x86_64 p11-kit-trust-0.26.1-1.el10.x86_64 package-notes-srpm-macros-0.5-13.el10.noarch pam-1.6.1-9.el10.x86_64 pam-libs-1.6.1-9.el10.x86_64 patch-2.7.6-26.el10.x86_64 pcre2-10.44-1.el10.3.x86_64 pcre2-syntax-10.44-1.el10.3.noarch perl-srpm-macros-1-57.el10.noarch pkgconf-2.1.0-3.el10.x86_64 pkgconf-m4-2.1.0-3.el10.noarch pkgconf-pkg-config-2.1.0-3.el10.x86_64 popt-1.19-8.el10.x86_64 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.x86_64 redhat-rpm-config-295-1.el10.noarch rpm-4.19.1.1-21.el10.x86_64 rpm-build-4.19.1.1-21.el10.x86_64 rpm-build-libs-4.19.1.1-21.el10.x86_64 rpm-libs-4.19.1.1-21.el10.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 rust-toolset-srpm-macros-1.92.0-1.el10.noarch sed-4.9-3.el10.x86_64 setup-2.14.5-7.el10.noarch shadow-utils-4.15.0-9.el10.x86_64 sqlite-libs-3.46.1-5.el10.x86_64 systemd-libs-257-21.el10.x86_64 tar-1.35-10.el10.x86_64 unzip-6.0-69.el10.x86_64 util-linux-2.40.2-13.el10.x86_64 util-linux-core-2.40.2-13.el10.x86_64 which-2.21-44.el10.x86_64 xz-5.6.2-4.el10.x86_64 xz-libs-5.6.2-4.el10.x86_64 zip-3.0-45.el10.x86_64 zlib-ng-compat-2.2.3-3.el10.x86_64 zstd-1.5.5-9.el10.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1769385600 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-x86_64-1769509085.666809/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-x86_64-1769509085.666809/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-x86_64-1769509085.666809/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-p7qk1sbd/bcftools/bcftools.spec) Config(child) 0 minutes 20 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-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/centos-stream+epel-10-x86_64-bootstrap-1769509085.666809/root. INFO: reusing tmpfs at /var/lib/mock/centos-stream+epel-10-x86_64-bootstrap-1769509085.666809/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-x86_64-1769509085.666809/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.x86_64 rpm-sequoia-1.9.0.3-1.el10.x86_64 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1769385600 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 9.1 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 22 kB/s | 4.5 kB 00:00 CentOS Stream 10 - AppStream 28 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 22 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 37 kB/s | 7.3 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 99 kB/s | 24 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 x86_64 14.3.1-4.2.el10 appstream 38 M gsl-devel x86_64 2.7.1-11.el10_0 epel 610 k htslib-devel x86_64 1.23-1.el10 copr_base 107 k htslib-tools x86_64 1.23-1.el10 copr_base 754 k make x86_64 1:4.4.1-9.el10 baseos 587 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 x86_64 4:5.40.2-514.el10 appstream 73 k zlib-ng-compat-devel x86_64 2.2.3-3.el10 appstream 36 k Installing dependencies: annobin-docs noarch 13.02-2.el10 appstream 87 k annobin-plugin-gcc x86_64 13.02-2.el10 appstream 997 k cmake-filesystem x86_64 3.31.8-1.el10 appstream 21 k cpp x86_64 14.3.1-4.2.el10 appstream 13 M emacs-filesystem noarch 1:29.4-12.el10 appstream 10 k expat x86_64 2.7.3-1.el10 baseos 120 k gcc-plugin-annobin x86_64 14.3.1-4.2.el10 appstream 69 k glibc-devel x86_64 2.39-99.el10 appstream 598 k groff-base x86_64 1.23.0-10.el10 baseos 1.1 M gsl x86_64 2.7.1-11.el10_0 epel 1.1 M htslib x86_64 1.23-1.el10 copr_base 593 k kernel-headers x86_64 6.12.0-191.el10 appstream 3.1 M libmpc x86_64 1.3.1-7.el10 appstream 71 k libxcrypt-devel x86_64 4.4.36-10.el10 appstream 30 k m4 x86_64 1.4.19-11.el10 appstream 305 k mpdecimal x86_64 2.5.1-12.el10 baseos 90 k ncurses x86_64 6.4-14.20240127.el10 baseos 423 k perl-AutoLoader noarch 5.74-514.el10 appstream 22 k perl-AutoSplit noarch 5.74-514.el10 appstream 22 k perl-B x86_64 1.89-514.el10 appstream 178 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 x86_64 2.189-512.el10 baseos 57 k perl-Devel-PPPort x86_64 3.72-512.el10 appstream 220 k perl-Digest noarch 1.20-511.el10 baseos 26 k perl-Digest-MD5 x86_64 2.59-6.el10 baseos 37 k perl-DynaLoader x86_64 1.56-514.el10 appstream 27 k perl-Encode x86_64 4:3.21-511.el10 baseos 1.1 M perl-Errno x86_64 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 x86_64 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 x86_64 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 x86_64 3.16-511.el10 baseos 31 k perl-Mozilla-CA noarch 20231213-5.el10 baseos 15 k perl-Net-SSLeay x86_64 1.94-8.el10 appstream 380 k perl-POSIX x86_64 2.20-514.el10 appstream 97 k perl-PathTools x86_64 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 x86_64 5:1.63-511.el10 baseos 74 k perl-SelectSaver noarch 1.02-514.el10 appstream 12 k perl-Socket x86_64 4:2.038-511.el10 baseos 56 k perl-Storable x86_64 1:3.32-511.el10 baseos 99 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 x86_64 4:5.40.2-514.el10 appstream 768 k perl-if noarch 0.61.000-514.el10 appstream 15 k perl-lib x86_64 0.65-514.el10 appstream 16 k perl-libnet noarch 3.15-512.el10 baseos 127 k perl-libs x86_64 4:5.40.2-514.el10 appstream 2.4 M perl-locale noarch 1.12-514.el10 appstream 14 k perl-mro x86_64 1.29-514.el10 appstream 31 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 x86_64 1:2.40-511.el10 appstream 59 k perl-threads-shared x86_64 1.69-511.el10 appstream 46 k perl-vars noarch 1.05-514.el10 appstream 14 k perl-version x86_64 8:0.99.32-4.el10 appstream 64 k python3 x86_64 3.12.12-3.el10 baseos 28 k python3-libs x86_64 3.12.12-3.el10 baseos 9.4 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 x86_64 5.4-3.el10 appstream 69 k systemtap-sdt-dtrace x86_64 5.4-3.el10 appstream 70 k tzdata noarch 2025c-1.el10 baseos 904 k Transaction Summary ================================================================================ Install 110 Packages Total download size: 84 M Installed size: 259 M Downloading Packages: (1/110): htslib-devel-1.23-1.el10.x86_64.rpm 6.8 MB/s | 107 kB 00:00 (2/110): htslib-1.23-1.el10.x86_64.rpm 32 MB/s | 593 kB 00:00 (3/110): htslib-tools-1.23-1.el10.x86_64.rpm 38 MB/s | 754 kB 00:00 (4/110): expat-2.7.3-1.el10.x86_64.rpm 12 MB/s | 120 kB 00:00 (5/110): mpdecimal-2.5.1-12.el10.x86_64.rpm 34 MB/s | 90 kB 00:00 (6/110): make-4.4.1-9.el10.x86_64.rpm 50 MB/s | 587 kB 00:00 (7/110): ncurses-6.4-14.20240127.el10.x86_64.rp 81 MB/s | 423 kB 00:00 (8/110): perl-Carp-1.54-511.el10.noarch.rpm 11 MB/s | 30 kB 00:00 (9/110): perl-Data-Dumper-2.189-512.el10.x86_64 29 MB/s | 57 kB 00:00 (10/110): perl-Digest-1.20-511.el10.noarch.rpm 13 MB/s | 26 kB 00:00 (11/110): perl-Digest-MD5-2.59-6.el10.x86_64.rp 18 MB/s | 37 kB 00:00 (12/110): perl-Encode-3.21-511.el10.x86_64.rpm 165 MB/s | 1.1 MB 00:00 (13/110): perl-Exporter-5.78-511.el10.noarch.rp 6.3 MB/s | 32 kB 00:00 (14/110): perl-File-Temp-0.231.100-512.el10.noa 40 MB/s | 60 kB 00:00 (15/110): perl-HTTP-Tiny-0.088-512.el10.noarch. 34 MB/s | 57 kB 00:00 (16/110): perl-Getopt-Long-2.58-3.el10.noarch.r 19 MB/s | 65 kB 00:00 (17/110): groff-base-1.23.0-10.el10.x86_64.rpm 37 MB/s | 1.1 MB 00:00 (18/110): perl-IO-Socket-IP-0.42-512.el10.noarc 18 MB/s | 43 kB 00:00 (19/110): perl-IO-Socket-SSL-2.085-3.el10.noarc 61 MB/s | 227 kB 00:00 (20/110): perl-MIME-Base64-3.16-511.el10.x86_64 15 MB/s | 31 kB 00:00 (21/110): perl-Mozilla-CA-20231213-5.el10.noarc 7.3 MB/s | 15 kB 00:00 (22/110): perl-Pod-Escapes-1.07-511.el10.noarch 8.9 MB/s | 21 kB 00:00 (23/110): perl-PathTools-3.91-512.el10.x86_64.r 25 MB/s | 85 kB 00:00 (24/110): perl-Pod-Perldoc-3.28.01-512.el10.noa 25 MB/s | 84 kB 00:00 (25/110): perl-Pod-Usage-2.03-511.el10.noarch.r 26 MB/s | 41 kB 00:00 (26/110): perl-Pod-Simple-3.45-511.el10.noarch. 68 MB/s | 218 kB 00:00 (27/110): perl-Scalar-List-Utils-1.63-511.el10. 27 MB/s | 74 kB 00:00 (28/110): perl-Socket-2.038-511.el10.x86_64.rpm 34 MB/s | 56 kB 00:00 (29/110): perl-Term-ANSIColor-5.01-512.el10.noa 29 MB/s | 49 kB 00:00 (30/110): perl-Storable-3.32-511.el10.x86_64.rp 35 MB/s | 99 kB 00:00 (31/110): perl-Term-Cap-1.18-511.el10.noarch.rp 7.6 MB/s | 23 kB 00:00 (32/110): perl-Text-ParseWords-3.31-511.el10.no 9.6 MB/s | 17 kB 00:00 (33/110): perl-Text-Tabs+Wrap-2024.001-511.el10 13 MB/s | 23 kB 00:00 (34/110): perl-Time-Local-1.350-511.el10.noarch 19 MB/s | 35 kB 00:00 (35/110): perl-constant-1.33-512.el10.noarch.rp 14 MB/s | 24 kB 00:00 (36/110): perl-URI-5.27-3.el10.noarch.rpm 43 MB/s | 134 kB 00:00 (37/110): perl-parent-0.241-512.el10.noarch.rpm 9.3 MB/s | 16 kB 00:00 (38/110): perl-libnet-3.15-512.el10.noarch.rpm 36 MB/s | 127 kB 00:00 (39/110): python3-3.12.12-3.el10.x86_64.rpm 18 MB/s | 28 kB 00:00 (40/110): perl-podlators-5.01-511.el10.noarch.r 40 MB/s | 124 kB 00:00 (41/110): python3-pyparsing-3.1.1-7.el10.noarch 24 MB/s | 269 kB 00:00 (42/110): python3-pip-wheel-23.3.2-7.el10.noarc 63 MB/s | 1.5 MB 00:00 (43/110): python3-libs-3.12.12-3.el10.x86_64.rp 279 MB/s | 9.4 MB 00:00 (44/110): tzdata-2025c-1.el10.noarch.rpm 37 MB/s | 904 kB 00:00 (45/110): annobin-docs-13.02-2.el10.noarch.rpm 7.1 MB/s | 87 kB 00:00 (46/110): annobin-plugin-gcc-13.02-2.el10.x86_6 132 MB/s | 997 kB 00:00 (47/110): autoconf-2.71-13.el10.noarch.rpm 95 MB/s | 736 kB 00:00 (48/110): cmake-filesystem-3.31.8-1.el10.x86_64 8.8 MB/s | 21 kB 00:00 (49/110): automake-1.16.5-20.el10.noarch.rpm 81 MB/s | 702 kB 00:00 (50/110): emacs-filesystem-29.4-12.el10.noarch. 6.3 MB/s | 10 kB 00:00 (51/110): gcc-plugin-annobin-14.3.1-4.2.el10.x8 19 MB/s | 69 kB 00:00 (52/110): glibc-devel-2.39-99.el10.x86_64.rpm 29 MB/s | 598 kB 00:00 (53/110): cpp-14.3.1-4.2.el10.x86_64.rpm 206 MB/s | 13 MB 00:00 (54/110): kernel-headers-6.12.0-191.el10.x86_64 66 MB/s | 3.1 MB 00:00 (55/110): libxcrypt-devel-4.4.36-10.el10.x86_64 4.6 MB/s | 30 kB 00:00 (56/110): libmpc-1.3.1-7.el10.x86_64.rpm 3.7 MB/s | 71 kB 00:00 (57/110): perl-AutoLoader-5.74-514.el10.noarch. 5.0 MB/s | 22 kB 00:00 (58/110): m4-1.4.19-11.el10.x86_64.rpm 31 MB/s | 305 kB 00:00 (59/110): perl-AutoSplit-5.74-514.el10.noarch.r 3.6 MB/s | 22 kB 00:00 (60/110): perl-B-1.89-514.el10.x86_64.rpm 44 MB/s | 178 kB 00:00 (61/110): perl-Class-Struct-0.68-514.el10.noarc 11 MB/s | 23 kB 00:00 (62/110): perl-Benchmark-1.25-514.el10.noarch.r 4.9 MB/s | 27 kB 00:00 (63/110): perl-DynaLoader-1.56-514.el10.x86_64. 18 MB/s | 27 kB 00:00 (64/110): perl-Devel-PPPort-3.72-512.el10.x86_6 46 MB/s | 220 kB 00:00 (65/110): perl-Errno-1.38-514.el10.x86_64.rpm 5.1 MB/s | 16 kB 00:00 (66/110): gcc-14.3.1-4.2.el10.x86_64.rpm 280 MB/s | 38 MB 00:00 (67/110): perl-ExtUtils-Command-7.70-513.el10.n 425 kB/s | 15 kB 00:00 (68/110): perl-ExtUtils-Constant-0.25-514.el10. 1.2 MB/s | 44 kB 00:00 (69/110): perl-ExtUtils-Embed-1.35-514.el10.noa 5.2 MB/s | 18 kB 00:00 (70/110): perl-ExtUtils-Install-2.22-511.el10.n 10 MB/s | 44 kB 00:00 (71/110): perl-ExtUtils-MakeMaker-7.70-513.el10 50 MB/s | 293 kB 00:00 (72/110): perl-ExtUtils-Manifest-1.75-511.el10. 10 MB/s | 35 kB 00:00 (73/110): perl-Fcntl-1.18-514.el10.x86_64.rpm 13 MB/s | 30 kB 00:00 (74/110): perl-File-Basename-2.86-514.el10.noar 9.6 MB/s | 18 kB 00:00 (75/110): perl-ExtUtils-ParseXS-3.51-512.el10.n 34 MB/s | 186 kB 00:00 (76/110): perl-File-Compare-1.100.800-514.el10. 5.4 MB/s | 14 kB 00:00 (77/110): perl-File-Copy-2.41-514.el10.noarch.r 7.8 MB/s | 21 kB 00:00 (78/110): perl-File-Find-1.44-514.el10.noarch.r 12 MB/s | 26 kB 00:00 (79/110): perl-File-Path-2.18-512.el10.noarch.r 20 MB/s | 35 kB 00:00 (80/110): perl-File-stat-1.14-514.el10.noarch.r 10 MB/s | 18 kB 00:00 (81/110): perl-FileHandle-2.05-514.el10.noarch. 9.7 MB/s | 16 kB 00:00 (82/110): perl-FindBin-1.54-514.el10.noarch.rpm 6.8 MB/s | 15 kB 00:00 (83/110): perl-Getopt-Std-1.14-514.el10.noarch. 6.4 MB/s | 16 kB 00:00 (84/110): perl-IPC-Open3-1.22-514.el10.noarch.r 14 MB/s | 23 kB 00:00 (85/110): perl-IO-1.55-514.el10.x86_64.rpm 23 MB/s | 81 kB 00:00 (86/110): perl-SelectSaver-1.02-514.el10.noarch 6.1 MB/s | 12 kB 00:00 (87/110): perl-Net-SSLeay-1.94-8.el10.x86_64.rp 85 MB/s | 380 kB 00:00 (88/110): perl-POSIX-2.20-514.el10.x86_64.rpm 27 MB/s | 97 kB 00:00 (89/110): perl-Symbol-1.09-514.el10.noarch.rpm 3.9 MB/s | 15 kB 00:00 (90/110): perl-Thread-Queue-3.14-511.el10.noarc 8.4 MB/s | 22 kB 00:00 (91/110): perl-base-2.27-514.el10.noarch.rpm 9.5 MB/s | 17 kB 00:00 (92/110): perl-Test-Harness-3.48-512.el10.noarc 51 MB/s | 284 kB 00:00 (93/110): perl-if-0.61.000-514.el10.noarch.rpm 9.0 MB/s | 15 kB 00:00 (94/110): perl-interpreter-5.40.2-514.el10.x86_ 21 MB/s | 73 kB 00:00 (95/110): perl-devel-5.40.2-514.el10.x86_64.rpm 104 MB/s | 768 kB 00:00 (96/110): perl-lib-0.65-514.el10.x86_64.rpm 4.1 MB/s | 16 kB 00:00 (97/110): perl-locale-1.12-514.el10.noarch.rpm 8.3 MB/s | 14 kB 00:00 (98/110): perl-libs-5.40.2-514.el10.x86_64.rpm 301 MB/s | 2.4 MB 00:00 (99/110): perl-mro-1.29-514.el10.x86_64.rpm 4.3 MB/s | 31 kB 00:00 (100/110): perl-overload-1.37-514.el10.noarch.r 8.3 MB/s | 46 kB 00:00 (101/110): perl-overloading-0.02-514.el10.noarc 7.9 MB/s | 14 kB 00:00 (102/110): perl-threads-2.40-511.el10.x86_64.rp 26 MB/s | 59 kB 00:00 (103/110): perl-threads-shared-1.69-511.el10.x8 19 MB/s | 46 kB 00:00 (104/110): perl-vars-1.05-514.el10.noarch.rpm 10 MB/s | 14 kB 00:00 (105/110): systemtap-sdt-devel-5.4-3.el10.x86_6 21 MB/s | 69 kB 00:00 (106/110): perl-version-0.99.32-4.el10.x86_64.r 16 MB/s | 64 kB 00:00 (107/110): systemtap-sdt-dtrace-5.4-3.el10.x86_ 20 MB/s | 70 kB 00:00 (108/110): zlib-ng-compat-devel-2.2.3-3.el10.x8 20 MB/s | 36 kB 00:00 (109/110): gsl-devel-2.7.1-11.el10_0.x86_64.rpm 8.5 MB/s | 610 kB 00:00 (110/110): gsl-2.7.1-11.el10_0.x86_64.rpm 15 MB/s | 1.1 MB 00:00 -------------------------------------------------------------------------------- Total 82 MB/s | 84 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-7.el10.x86_64 1/110 Installing : htslib-1.23-1.el10.x86_64 2/110 Installing : cpp-14.3.1-4.2.el10.x86_64 3/110 Installing : gsl-2.7.1-11.el10_0.x86_64 4/110 Installing : m4-1.4.19-11.el10.x86_64 5/110 Installing : kernel-headers-6.12.0-191.el10.x86_64 6/110 Installing : libxcrypt-devel-4.4.36-10.el10.x86_64 7/110 Installing : glibc-devel-2.39-99.el10.x86_64 8/110 Installing : emacs-filesystem-1:29.4-12.el10.noarch 9/110 Installing : cmake-filesystem-3.31.8-1.el10.x86_64 10/110 Installing : annobin-docs-13.02-2.el10.noarch 11/110 Installing : tzdata-2025c-1.el10.noarch 12/110 Installing : python3-pip-wheel-23.3.2-7.el10.noarch 13/110 Installing : ncurses-6.4-14.20240127.el10.x86_64 14/110 Installing : mpdecimal-2.5.1-12.el10.x86_64 15/110 Installing : make-1:4.4.1-9.el10.x86_64 16/110 Installing : gcc-14.3.1-4.2.el10.x86_64 17/110 Running scriptlet: gcc-14.3.1-4.2.el10.x86_64 17/110 Running scriptlet: groff-base-1.23.0-10.el10.x86_64 18/110 Installing : groff-base-1.23.0-10.el10.x86_64 18/110 Running scriptlet: groff-base-1.23.0-10.el10.x86_64 18/110 Installing : perl-Digest-1.20-511.el10.noarch 19/110 Installing : perl-Digest-MD5-2.59-6.el10.x86_64 20/110 Installing : perl-B-1.89-514.el10.x86_64 21/110 Installing : perl-FileHandle-2.05-514.el10.noarch 22/110 Installing : perl-Data-Dumper-2.189-512.el10.x86_64 23/110 Installing : perl-libnet-3.15-512.el10.noarch 24/110 Installing : perl-AutoLoader-5.74-514.el10.noarch 25/110 Installing : perl-URI-5.27-3.el10.noarch 26/110 Installing : perl-Text-Tabs+Wrap-2024.001-511.el10.noarch 27/110 Installing : perl-Time-Local-2:1.350-511.el10.noarch 28/110 Installing : perl-Mozilla-CA-20231213-5.el10.noarch 29/110 Installing : perl-if-0.61.000-514.el10.noarch 30/110 Installing : perl-locale-1.12-514.el10.noarch 31/110 Installing : perl-IO-Socket-IP-0.42-512.el10.noarch 32/110 Installing : perl-Pod-Escapes-1:1.07-511.el10.noarch 33/110 Installing : perl-File-Path-2.18-512.el10.noarch 34/110 Installing : perl-IO-Socket-SSL-2.085-3.el10.noarch 35/110 Installing : perl-Net-SSLeay-1.94-8.el10.x86_64 36/110 Installing : perl-Term-ANSIColor-5.01-512.el10.noarch 37/110 Installing : perl-Class-Struct-0.68-514.el10.noarch 38/110 Installing : perl-POSIX-2.20-514.el10.x86_64 39/110 Installing : perl-IPC-Open3-1.22-514.el10.noarch 40/110 Installing : perl-Term-Cap-1.18-511.el10.noarch 41/110 Installing : perl-File-Temp-1:0.231.100-512.el10.noarch 42/110 Installing : perl-HTTP-Tiny-0.088-512.el10.noarch 43/110 Installing : perl-Pod-Simple-1:3.45-511.el10.noarch 44/110 Installing : perl-Socket-4:2.038-511.el10.x86_64 45/110 Installing : perl-SelectSaver-1.02-514.el10.noarch 46/110 Installing : perl-Symbol-1.09-514.el10.noarch 47/110 Installing : perl-File-stat-1.14-514.el10.noarch 48/110 Installing : perl-podlators-1:5.01-511.el10.noarch 49/110 Installing : perl-Pod-Perldoc-3.28.01-512.el10.noarch 50/110 Installing : perl-Text-ParseWords-3.31-511.el10.noarch 51/110 Installing : perl-Fcntl-1.18-514.el10.x86_64 52/110 Installing : perl-base-2.27-514.el10.noarch 53/110 Installing : perl-mro-1.29-514.el10.x86_64 54/110 Installing : perl-IO-1.55-514.el10.x86_64 55/110 Installing : perl-overloading-0.02-514.el10.noarch 56/110 Installing : perl-Pod-Usage-4:2.03-511.el10.noarch 57/110 Installing : perl-MIME-Base64-3.16-511.el10.x86_64 58/110 Installing : perl-Scalar-List-Utils-5:1.63-511.el10.x86_64 59/110 Installing : perl-constant-1.33-512.el10.noarch 60/110 Installing : perl-parent-1:0.241-512.el10.noarch 61/110 Installing : perl-Errno-1.38-514.el10.x86_64 62/110 Installing : perl-File-Basename-2.86-514.el10.noarch 63/110 Installing : perl-Getopt-Std-1.14-514.el10.noarch 64/110 Installing : perl-Storable-1:3.32-511.el10.x86_64 65/110 Installing : perl-overload-1.37-514.el10.noarch 66/110 Installing : perl-vars-1.05-514.el10.noarch 67/110 Installing : perl-Getopt-Long-1:2.58-3.el10.noarch 68/110 Installing : perl-Carp-1.54-511.el10.noarch 69/110 Installing : perl-Exporter-5.78-511.el10.noarch 70/110 Installing : perl-PathTools-3.91-512.el10.x86_64 71/110 Installing : perl-DynaLoader-1.56-514.el10.x86_64 72/110 Installing : perl-Encode-4:3.21-511.el10.x86_64 73/110 Installing : perl-libs-4:5.40.2-514.el10.x86_64 74/110 Installing : perl-interpreter-4:5.40.2-514.el10.x86_64 75/110 Installing : perl-File-Find-1.44-514.el10.noarch 76/110 Installing : perl-File-Copy-2.41-514.el10.noarch 77/110 Installing : perl-File-Compare-1.100.800-514.el10.noarch 78/110 Installing : perl-ExtUtils-ParseXS-1:3.51-512.el10.noarch 79/110 Installing : perl-threads-1:2.40-511.el10.x86_64 80/110 Installing : perl-threads-shared-1.69-511.el10.x86_64 81/110 Installing : perl-Thread-Queue-3.14-511.el10.noarch 82/110 Installing : autoconf-2.71-13.el10.noarch 83/110 Installing : automake-1.16.5-20.el10.noarch 84/110 Installing : perl-ExtUtils-Command-2:7.70-513.el10.noarch 85/110 Installing : perl-ExtUtils-Manifest-1:1.75-511.el10.noarch 86/110 Installing : perl-AutoSplit-5.74-514.el10.noarch 87/110 Installing : perl-Benchmark-1.25-514.el10.noarch 88/110 Installing : perl-Test-Harness-1:3.48-512.el10.noarch 89/110 Installing : perl-Devel-PPPort-3.72-512.el10.x86_64 90/110 Installing : perl-ExtUtils-Constant-0.25-514.el10.noarch 91/110 Installing : perl-lib-0.65-514.el10.x86_64 92/110 Installing : perl-version-8:0.99.32-4.el10.x86_64 93/110 Installing : expat-2.7.3-1.el10.x86_64 94/110 Installing : python3-3.12.12-3.el10.x86_64 95/110 Installing : python3-libs-3.12.12-3.el10.x86_64 96/110 Installing : python3-pyparsing-3.1.1-7.el10.noarch 97/110 Installing : systemtap-sdt-dtrace-5.4-3.el10.x86_64 98/110 Installing : systemtap-sdt-devel-5.4-3.el10.x86_64 99/110 Installing : perl-ExtUtils-Install-2.22-511.el10.noarch 100/110 Installing : perl-devel-4:5.40.2-514.el10.x86_64 101/110 Installing : perl-ExtUtils-MakeMaker-2:7.70-513.el10.noarch 102/110 Installing : perl-ExtUtils-Embed-1.35-514.el10.noarch 103/110 Installing : gsl-devel-2.7.1-11.el10_0.x86_64 104/110 Installing : perl-FindBin-1.54-514.el10.noarch 105/110 Installing : annobin-plugin-gcc-13.02-2.el10.x86_64 106/110 Running scriptlet: annobin-plugin-gcc-13.02-2.el10.x86_64 106/110 Installing : gcc-plugin-annobin-14.3.1-4.2.el10.x86_64 107/110 Running scriptlet: gcc-plugin-annobin-14.3.1-4.2.el10.x86_64 107/110 Installing : zlib-ng-compat-devel-2.2.3-3.el10.x86_64 108/110 Installing : htslib-devel-1.23-1.el10.x86_64 109/110 Installing : htslib-tools-1.23-1.el10.x86_64 110/110 Running scriptlet: htslib-tools-1.23-1.el10.x86_64 110/110 Installed: annobin-docs-13.02-2.el10.noarch annobin-plugin-gcc-13.02-2.el10.x86_64 autoconf-2.71-13.el10.noarch automake-1.16.5-20.el10.noarch cmake-filesystem-3.31.8-1.el10.x86_64 cpp-14.3.1-4.2.el10.x86_64 emacs-filesystem-1:29.4-12.el10.noarch expat-2.7.3-1.el10.x86_64 gcc-14.3.1-4.2.el10.x86_64 gcc-plugin-annobin-14.3.1-4.2.el10.x86_64 glibc-devel-2.39-99.el10.x86_64 groff-base-1.23.0-10.el10.x86_64 gsl-2.7.1-11.el10_0.x86_64 gsl-devel-2.7.1-11.el10_0.x86_64 htslib-1.23-1.el10.x86_64 htslib-devel-1.23-1.el10.x86_64 htslib-tools-1.23-1.el10.x86_64 kernel-headers-6.12.0-191.el10.x86_64 libmpc-1.3.1-7.el10.x86_64 libxcrypt-devel-4.4.36-10.el10.x86_64 m4-1.4.19-11.el10.x86_64 make-1:4.4.1-9.el10.x86_64 mpdecimal-2.5.1-12.el10.x86_64 ncurses-6.4-14.20240127.el10.x86_64 perl-AutoLoader-5.74-514.el10.noarch perl-AutoSplit-5.74-514.el10.noarch perl-B-1.89-514.el10.x86_64 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.x86_64 perl-Devel-PPPort-3.72-512.el10.x86_64 perl-Digest-1.20-511.el10.noarch perl-Digest-MD5-2.59-6.el10.x86_64 perl-DynaLoader-1.56-514.el10.x86_64 perl-Encode-4:3.21-511.el10.x86_64 perl-Errno-1.38-514.el10.x86_64 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.x86_64 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.x86_64 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.x86_64 perl-Mozilla-CA-20231213-5.el10.noarch perl-Net-SSLeay-1.94-8.el10.x86_64 perl-POSIX-2.20-514.el10.x86_64 perl-PathTools-3.91-512.el10.x86_64 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.x86_64 perl-SelectSaver-1.02-514.el10.noarch perl-Socket-4:2.038-511.el10.x86_64 perl-Storable-1:3.32-511.el10.x86_64 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.x86_64 perl-if-0.61.000-514.el10.noarch perl-interpreter-4:5.40.2-514.el10.x86_64 perl-lib-0.65-514.el10.x86_64 perl-libnet-3.15-512.el10.noarch perl-libs-4:5.40.2-514.el10.x86_64 perl-locale-1.12-514.el10.noarch perl-mro-1.29-514.el10.x86_64 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.x86_64 perl-threads-shared-1.69-511.el10.x86_64 perl-vars-1.05-514.el10.noarch perl-version-8:0.99.32-4.el10.x86_64 python3-3.12.12-3.el10.x86_64 python3-libs-3.12.12-3.el10.x86_64 python3-pip-wheel-23.3.2-7.el10.noarch python3-pyparsing-3.1.1-7.el10.noarch systemtap-sdt-devel-5.4-3.el10.x86_64 systemtap-sdt-dtrace-5.4-3.el10.x86_64 tzdata-2025c-1.el10.noarch zlib-ng-compat-devel-2.2.3-3.el10.x86_64 Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1769385600 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 22 kB/s | 1.5 kB 00:00 CentOS Stream 10 - BaseOS 24 kB/s | 4.5 kB 00:00 CentOS Stream 10 - AppStream 27 kB/s | 5.5 kB 00:00 CentOS Stream 10 - CRB 23 kB/s | 4.4 kB 00:00 CentOS Stream 10 - Extras packages 39 kB/s | 7.3 kB 00:00 Extra Packages for Enterprise Linux 10 - x86_64 97 kB/s | 24 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.x86_64 is already installed. Package gsl-devel-2.7.1-11.el10_0.x86_64 is already installed. Package htslib-devel-1.23-1.el10.x86_64 is already installed. Package htslib-tools-1.23-1.el10.x86_64 is already installed. Package make-1:4.4.1-9.el10.x86_64 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.x86_64 is already installed. Package zlib-ng-compat-devel-2.2.3-3.el10.x86_64 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1769385600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.XabV75 + 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 . Patch #0 (bcftools-1.23-perl-fix-stray-errors-ldflags.patch): + echo '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.FZ4qYU + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./htslib-1.23/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./htslib-1.23/config.sub ++ basename ./htslib-1.23/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./htslib-1.23/config.sub '/usr/lib/rpm/redhat/config.sub' -> './htslib-1.23/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for x86_64-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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection 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-m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -I. -DUSE_GPL -c -o main.o main.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 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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.wYhudE + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64 ++ dirname /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64 + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/bin /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/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.x86_64/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/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.x86_64 --unique-debug-src-base bcftools-1.23-1.el10.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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.x86_64 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.ktru2s + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 ' + 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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -m64 -march=x86-64-v3 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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)?(/lp64d)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x00007f4724c04000) + 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_usage: bcftools ./test/test.pl: module IO::Pty not found; skipping usage tests test_tabix: tabix /tmp/wqLK3Tx6qo/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/wqLK3Tx6qo/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.23/bcftools view -H /tmp/wqLK3Tx6qo/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/wqLK3Tx6qo/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/wqLK3Tx6qo/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/wqLK3Tx6qo/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/wqLK3Tx6qo/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/wqLK3Tx6qo/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -s /tmp/wqLK3Tx6qo/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.23/bcftools index -n /tmp/wqLK3Tx6qo/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/check.1.chk /tmp/wqLK3Tx6qo/check.2.chk /tmp/wqLK3Tx6qo/check.3.chk /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/stats.a.vcf.gz /tmp/wqLK3Tx6qo/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s B /tmp/wqLK3Tx6qo/stats.a.vcf.gz /tmp/wqLK3Tx6qo/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.23/bcftools stats -s - /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/isec.match-id.1.1.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/isec.match-id.1.1.vcf.gz /tmp/wqLK3Tx6qo/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 /tmp/wqLK3Tx6qo/isec.a.vcf.gz /tmp/wqLK3Tx6qo/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/wqLK3Tx6qo/isec.a.vcf.gz /tmp/wqLK3Tx6qo/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -c both /tmp/wqLK3Tx6qo/isec.a.vcf.gz /tmp/wqLK3Tx6qo/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -n =2 -c any /tmp/wqLK3Tx6qo/isec.a.vcf.gz /tmp/wqLK3Tx6qo/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.23/bcftools isec -C -c any /tmp/wqLK3Tx6qo/isec.a.vcf.gz /tmp/wqLK3Tx6qo/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.23/bcftools isec --no-version -T /tmp/wqLK3Tx6qo/isec.tab.gz /tmp/wqLK3Tx6qo/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.23/bcftools isec -Ob -T /tmp/wqLK3Tx6qo/isec.tab.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/isec-miss.1.1.vcf.gz /tmp/wqLK3Tx6qo/isec-miss.1.2.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/isec-miss.1.1.vcf.gz /tmp/wqLK3Tx6qo/isec-miss.1.2.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/isec-miss.2.1.vcf.gz /tmp/wqLK3Tx6qo/isec-miss.2.2.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/isec-miss.2.1.vcf.gz /tmp/wqLK3Tx6qo/isec-miss.2.2.vcf.gz /tmp/wqLK3Tx6qo/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version /tmp/wqLK3Tx6qo/merge.broken-gvcf.a.vcf.gz /tmp/wqLK3Tx6qo/merge.broken-gvcf.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.broken-gvcf.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.broken-gvcf.a.bcf /tmp/wqLK3Tx6qo/merge.broken-gvcf.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.broken-gvcf.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.symbolic.1.a.vcf.gz /tmp/wqLK3Tx6qo/merge.symbolic.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.symbolic.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.symbolic.1.a.bcf /tmp/wqLK3Tx6qo/merge.symbolic.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.symbolic.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.multiallelics.1.a.vcf.gz /tmp/wqLK3Tx6qo/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/wqLK3Tx6qo/merge.multiallelics.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.multiallelics.1.a.bcf /tmp/wqLK3Tx6qo/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/wqLK3Tx6qo/merge.multiallelics.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.multiallelics.1.a.vcf.gz /tmp/wqLK3Tx6qo/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/wqLK3Tx6qo/merge.multiallelics.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.multiallelics.1.a.bcf /tmp/wqLK3Tx6qo/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/wqLK3Tx6qo/merge.multiallelics.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.12.a.vcf.gz /tmp/wqLK3Tx6qo/merge.12.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/wqLK3Tx6qo/merge.12.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.12.a.bcf /tmp/wqLK3Tx6qo/merge.12.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge none /tmp/wqLK3Tx6qo/merge.12.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.12.a.vcf.gz /tmp/wqLK3Tx6qo/merge.12.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/wqLK3Tx6qo/merge.12.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.12.a.bcf /tmp/wqLK3Tx6qo/merge.12.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --merge both /tmp/wqLK3Tx6qo/merge.12.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.phased.1.a.vcf.gz /tmp/wqLK3Tx6qo/merge.phased.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.phased.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.phased.1.a.bcf /tmp/wqLK3Tx6qo/merge.phased.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.phased.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.11.a.vcf.gz /tmp/wqLK3Tx6qo/merge.11.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.11.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.11.a.bcf /tmp/wqLK3Tx6qo/merge.11.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.11.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.join.a.vcf.gz /tmp/wqLK3Tx6qo/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AF:join /tmp/wqLK3Tx6qo/merge.join.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.join.a.bcf /tmp/wqLK3Tx6qo/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -i AF:join /tmp/wqLK3Tx6qo/merge.join.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-single /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-single /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.vcf.gz /tmp/wqLK3Tx6qo/merge.LPL.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wqLK3Tx6qo/merge.LPL.a.bcf /tmp/wqLK3Tx6qo/merge.LPL.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.a.vcf.gz /tmp/wqLK3Tx6qo/merge.b.vcf.gz /tmp/wqLK3Tx6qo/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/wqLK3Tx6qo/merge.a.vcf.gz /tmp/wqLK3Tx6qo/merge.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.a.bcf /tmp/wqLK3Tx6qo/merge.b.bcf /tmp/wqLK3Tx6qo/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/wqLK3Tx6qo/merge.a.bcf /tmp/wqLK3Tx6qo/merge.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.a.vcf.gz /tmp/wqLK3Tx6qo/merge.b.vcf.gz /tmp/wqLK3Tx6qo/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wqLK3Tx6qo/merge.a.vcf.gz /tmp/wqLK3Tx6qo/merge.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.a.bcf /tmp/wqLK3Tx6qo/merge.b.bcf /tmp/wqLK3Tx6qo/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wqLK3Tx6qo/merge.a.bcf /tmp/wqLK3Tx6qo/merge.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.a.vcf.gz /tmp/wqLK3Tx6qo/merge.b.vcf.gz /tmp/wqLK3Tx6qo/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -0 /tmp/wqLK3Tx6qo/merge.a.vcf.gz /tmp/wqLK3Tx6qo/merge.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.a.bcf /tmp/wqLK3Tx6qo/merge.b.bcf /tmp/wqLK3Tx6qo/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -0 /tmp/wqLK3Tx6qo/merge.a.bcf /tmp/wqLK3Tx6qo/merge.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.bcf /tmp/wqLK3Tx6qo/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m none /tmp/wqLK3Tx6qo/merge.2.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.bcf /tmp/wqLK3Tx6qo/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m both /tmp/wqLK3Tx6qo/merge.2.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.2.a.bcf /tmp/wqLK3Tx6qo/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m all /tmp/wqLK3Tx6qo/merge.2.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.3.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.3.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.3.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.3.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.4.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.4.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.4.a.bcf /tmp/wqLK3Tx6qo/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples -m id /tmp/wqLK3Tx6qo/merge.4.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gvcf.merge.1.vcf.gz /tmp/wqLK3Tx6qo/gvcf.merge.2.vcf.gz /tmp/wqLK3Tx6qo/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/gvcf.merge.1.vcf.gz /tmp/wqLK3Tx6qo/gvcf.merge.2.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gvcf.merge.1.bcf /tmp/wqLK3Tx6qo/gvcf.merge.2.bcf /tmp/wqLK3Tx6qo/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/gvcf.merge.1.bcf /tmp/wqLK3Tx6qo/gvcf.merge.2.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.2.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.3.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.3.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.4.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.4.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.4.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.4.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.5.a.vcf.gz /tmp/wqLK3Tx6qo/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.5.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.5.a.bcf /tmp/wqLK3Tx6qo/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.5.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.6.a.vcf.gz /tmp/wqLK3Tx6qo/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.6.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.6.a.bcf /tmp/wqLK3Tx6qo/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.6.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.7.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.7.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.7.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.7.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.8.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.8.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.8.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.8.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.7.a.vcf.gz /tmp/wqLK3Tx6qo/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/wqLK3Tx6qo/merge.7.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.7.a.bcf /tmp/wqLK3Tx6qo/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --force-samples /tmp/wqLK3Tx6qo/merge.7.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9d.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9d.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9d.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9d.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9d.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9c.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.9d.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9d.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.9a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9c.bcf /tmp/wqLK3Tx6qo/merge.gvcf.9d.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.noidx.a.vcf.gz /tmp/wqLK3Tx6qo/merge.noidx.b.vcf.gz /tmp/wqLK3Tx6qo/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.noidx.a.vcf.gz /tmp/wqLK3Tx6qo/merge.noidx.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.noidx.a.bcf /tmp/wqLK3Tx6qo/merge.noidx.b.bcf /tmp/wqLK3Tx6qo/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.noidx.a.bcf /tmp/wqLK3Tx6qo/merge.noidx.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.noidx.a.bcf /tmp/wqLK3Tx6qo/merge.noidx.b.bcf /tmp/wqLK3Tx6qo/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --no-index /tmp/wqLK3Tx6qo/merge.noidx.a.bcf /tmp/wqLK3Tx6qo/merge.noidx.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.8.a.vcf.gz /tmp/wqLK3Tx6qo/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.8.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.8.a.bcf /tmp/wqLK3Tx6qo/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.8.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.8.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.8.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.8.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.8.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.9.a.vcf.gz /tmp/wqLK3Tx6qo/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.9.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.9.a.bcf /tmp/wqLK3Tx6qo/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob /tmp/wqLK3Tx6qo/merge.9.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.9.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.9.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.9.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.9.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.vcf.gz /tmp/wqLK3Tx6qo/merge.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/wqLK3Tx6qo/merge.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.bcf /tmp/wqLK3Tx6qo/merge.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m none /tmp/wqLK3Tx6qo/merge.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.vcf.gz /tmp/wqLK3Tx6qo/merge.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m both /tmp/wqLK3Tx6qo/merge.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.bcf /tmp/wqLK3Tx6qo/merge.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m both /tmp/wqLK3Tx6qo/merge.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.10.a.bcf /tmp/wqLK3Tx6qo/merge.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wqLK3Tx6qo/merge.10.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.mrules.1.a.vcf.gz /tmp/wqLK3Tx6qo/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.mrules.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.mrules.1.a.bcf /tmp/wqLK3Tx6qo/merge.mrules.1.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.mrules.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.mrules.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.mrules.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.mrules.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.mrules.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.5.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.5.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.5.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.5.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.5.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.5.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.5.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wqLK3Tx6qo/merge.gvcf.5.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.11.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.11.b.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.11.a.vcf.gz /tmp/wqLK3Tx6qo/merge.gvcf.11.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.11.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.11.b.bcf /tmp/wqLK3Tx6qo/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.23/bcftools merge --no-version -Ob --gvcf - /tmp/wqLK3Tx6qo/merge.gvcf.11.a.bcf /tmp/wqLK3Tx6qo/merge.gvcf.11.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/smpl-count.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.15.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.14.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.14.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.14.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.func.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.string.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.string.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.gtidx.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.header.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-or.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/query.filter-or.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.filter.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.filter.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.sort.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.sort.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -S lex /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --force /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m- --keep-sum AD /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m+ -s /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d all /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d none /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d exact /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d indels /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d both /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -d snps /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/atomize.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.5.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - --multi-overlaps . /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.m-any.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.phased-split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.phased-join.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.string-tags.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m -any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.split.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.merge.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +any /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/norm.merge.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.23/bcftools norm --no-version -m +both /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -HAA /tmp/wqLK3Tx6qo/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version /tmp/wqLK3Tx6qo/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -f PASS -Xks NA00003 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -xs NA00003 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -p /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -P /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -GVsnps /tmp/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -GVsnps /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -s ^NA00003 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -G /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -a /tmp/wqLK3Tx6qo/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -a /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asA /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asB /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -asA /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i'TXT0="text"' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob -i 'POS>=3062917' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ht 2 /tmp/wqLK3Tx6qo/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ht 3 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -c6:nonmajor /tmp/wqLK3Tx6qo/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -q0.3:major /tmp/wqLK3Tx6qo/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -H -a /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/mpileup.2.vcf.gz .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/mpileup.2.vcf.gz .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/mpileup.2.vcf.gz .. ok test_vcf_head2: /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wqLK3Tx6qo/regions.tab.gz /tmp/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wqLK3Tx6qo/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wqLK3Tx6qo/regions.tab.gz /tmp/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wqLK3Tx6qo/regions.bed /tmp/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wqLK3Tx6qo/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wqLK3Tx6qo/regions.bed /tmp/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wqLK3Tx6qo/regions.bed.gz /tmp/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wqLK3Tx6qo/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.23/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wqLK3Tx6qo/regions.bed.gz /tmp/wqLK3Tx6qo/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.23/bcftools annotate -a /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots4.vcf.gz -c +INFO /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots4.vcf.gz -c +INFO /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots11.vcf.gz -c FMT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots11.vcf.gz -c FMT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /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/wqLK3Tx6qo/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate20.src.vcf.gz -c FMT/GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate20.src.vcf.gz -c FMT/GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate20.src.vcf.gz -c +FMT/GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate20.src.vcf.gz -c +FMT/GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate20.src.vcf.gz -c -FMT/GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate20.src.vcf.gz -c -FMT/GT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate24.src.vcf.gz -c XX /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annotate24.src.vcf.gz -c XX /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.vcf.gz -c ALT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.vcf.gz -c ALT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.vcf.gz -c +ALT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.vcf.gz -c +ALT /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /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/wqLK3Tx6qo/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -i /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.23/test/norm.fa -i /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.1 && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.2 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.2.txt && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.3 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.4 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.5 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.6 -S /builddir/build/BUILD/bcftools-1.23/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.1.7 -G /builddir/build/BUILD/bcftools-1.23/test/split.grp.1.1.txt && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/split.2.1 && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/scatter.1.1 -n 3 && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/scatter.1.2 -s 21,22 && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/scatter.1.3 -s 21,22 -x X && cd /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.1.a.vcf.gz /tmp/wqLK3Tx6qo/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G /tmp/wqLK3Tx6qo/concat.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.1.a.vcf.gz /tmp/wqLK3Tx6qo/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob /tmp/wqLK3Tx6qo/concat.1.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.1.a.bcf /tmp/wqLK3Tx6qo/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob /tmp/wqLK3Tx6qo/concat.1.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.2.a.vcf.gz /tmp/wqLK3Tx6qo/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -a /tmp/wqLK3Tx6qo/concat.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.2.a.bcf /tmp/wqLK3Tx6qo/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -a /tmp/wqLK3Tx6qo/concat.2.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.2.a.vcf.gz /tmp/wqLK3Tx6qo/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -aD /tmp/wqLK3Tx6qo/concat.2.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.2.a.bcf /tmp/wqLK3Tx6qo/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -aD /tmp/wqLK3Tx6qo/concat.2.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.3.a.vcf.gz /tmp/wqLK3Tx6qo/concat.3.b.vcf.gz /tmp/wqLK3Tx6qo/concat.3.0.vcf.gz /tmp/wqLK3Tx6qo/concat.3.c.vcf.gz /tmp/wqLK3Tx6qo/concat.3.d.vcf.gz /tmp/wqLK3Tx6qo/concat.3.e.vcf.gz /tmp/wqLK3Tx6qo/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/wqLK3Tx6qo/concat.3.a.vcf.gz /tmp/wqLK3Tx6qo/concat.3.b.vcf.gz /tmp/wqLK3Tx6qo/concat.3.0.vcf.gz /tmp/wqLK3Tx6qo/concat.3.c.vcf.gz /tmp/wqLK3Tx6qo/concat.3.d.vcf.gz /tmp/wqLK3Tx6qo/concat.3.e.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.3.a.bcf /tmp/wqLK3Tx6qo/concat.3.b.bcf /tmp/wqLK3Tx6qo/concat.3.0.bcf /tmp/wqLK3Tx6qo/concat.3.c.bcf /tmp/wqLK3Tx6qo/concat.3.d.bcf /tmp/wqLK3Tx6qo/concat.3.e.bcf /tmp/wqLK3Tx6qo/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/wqLK3Tx6qo/concat.3.a.bcf /tmp/wqLK3Tx6qo/concat.3.b.bcf /tmp/wqLK3Tx6qo/concat.3.0.bcf /tmp/wqLK3Tx6qo/concat.3.c.bcf /tmp/wqLK3Tx6qo/concat.3.d.bcf /tmp/wqLK3Tx6qo/concat.3.e.bcf /tmp/wqLK3Tx6qo/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1963640177 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat --naive-force /tmp/wqLK3Tx6qo/naive_concat.0.bcf /tmp/wqLK3Tx6qo/naive_concat.1.bcf /tmp/wqLK3Tx6qo/naive_concat.2.bcf /tmp/wqLK3Tx6qo/naive_concat.3.bcf /tmp/wqLK3Tx6qo/naive_concat.4.bcf /tmp/wqLK3Tx6qo/naive_concat.5.bcf /tmp/wqLK3Tx6qo/naive_concat.6.bcf /tmp/wqLK3Tx6qo/naive_concat.7.bcf /tmp/wqLK3Tx6qo/naive_concat.8.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/naive_concat.0.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.1.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.2.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.3.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.4.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.5.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.6.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.7.vcf.gz /tmp/wqLK3Tx6qo/naive_concat.8.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.4.a.vcf.gz /tmp/wqLK3Tx6qo/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l /tmp/wqLK3Tx6qo/concat.4.a.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.4.a.bcf /tmp/wqLK3Tx6qo/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l /tmp/wqLK3Tx6qo/concat.4.a.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.5.a.vcf.gz /tmp/wqLK3Tx6qo/concat.5.b.vcf.gz /tmp/wqLK3Tx6qo/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/wqLK3Tx6qo/concat.5.a.vcf.gz /tmp/wqLK3Tx6qo/concat.5.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.5.a.bcf /tmp/wqLK3Tx6qo/concat.5.b.bcf /tmp/wqLK3Tx6qo/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-warn /tmp/wqLK3Tx6qo/concat.5.a.bcf /tmp/wqLK3Tx6qo/concat.5.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.5.a.bcf /tmp/wqLK3Tx6qo/concat.5.b.bcf /tmp/wqLK3Tx6qo/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -l --ligate-force /tmp/wqLK3Tx6qo/concat.5.a.bcf /tmp/wqLK3Tx6qo/concat.5.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.5.a.vcf.gz /tmp/wqLK3Tx6qo/concat.5.b.vcf.gz /tmp/wqLK3Tx6qo/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G -a -D /tmp/wqLK3Tx6qo/concat.5.a.vcf.gz /tmp/wqLK3Tx6qo/concat.5.b.vcf.gz /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/concat.5.a.bcf /tmp/wqLK3Tx6qo/concat.5.b.bcf /tmp/wqLK3Tx6qo/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.23/bcftools concat -Ob -G -a -D /tmp/wqLK3Tx6qo/concat.5.a.bcf /tmp/wqLK3Tx6qo/concat.5.b.bcf /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/empty.bcf | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.23/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/rename.map -Ov /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/rename.map -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.23/bcftools view -Ob /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/consensus.1.chain.new >/dev/null; cat /tmp/wqLK3Tx6qo/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/consensus.2.chain.new >/dev/null; cat /tmp/wqLK3Tx6qo/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/consensus.3.chain.new >/dev/null; cat /tmp/wqLK3Tx6qo/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -H 1 -c /tmp/wqLK3Tx6qo/consensus.4.chain.new >/dev/null; cat /tmp/wqLK3Tx6qo/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/wqLK3Tx6qo/consensus8.bcf -f /builddir/build/BUILD/bcftools-1.23/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.23/bcftools consensus /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.gvcf.a.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck --keep-refs /tmp/wqLK3Tx6qo/gtcheck.gvcf.b.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/wqLK3Tx6qo/gtcheck.gvcf.a.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/wqLK3Tx6qo/gtcheck.gvcf.b.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/wqLK3Tx6qo/gtcheck.2.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck -e 0 /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.1.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/wqLK3Tx6qo/gtcheck.ntop.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/gtcheck.ntop.vcf.gz -g /tmp/wqLK3Tx6qo/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.23/bcftools gtcheck /tmp/wqLK3Tx6qo/gtcheck.5.vcf.gz -g /tmp/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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/wqLK3Tx6qo/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.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.zq7to4 + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/doc/bcftools + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/doc/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.23/AUTHORS /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/doc/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.23/NEWS /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.p7wMQv + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/licenses/bcftools + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/licenses/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.23/LICENSE /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.23-1.el10 bcftools(x86-64) = 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 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(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_2.4)(64bit) libc.so.6(GLIBC_2.7)(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_2.2.5)(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.x86_64 Provides: bcftools-debugsource = 1.23-1.el10 bcftools-debugsource(x86-64) = 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.x86_64 Provides: bcftools-debuginfo = 1.23-1.el10 bcftools-debuginfo(x86-64) = 1.23-1.el10 debuginfo(build-id) = 01856b1a311fbae2fd12e3437f41323a804a70f6 debuginfo(build-id) = 02d6b02daf16784de971ebfb0f161b69d1f94c67 debuginfo(build-id) = 0f7e734be05ffb883ddc55acc78ca227ea7fceb6 debuginfo(build-id) = 151d914857b8e7f99316dcbf467730f932e8c7b7 debuginfo(build-id) = 1a9e4c1d88c86ecb2fda79f2f8cd4d2db5d91550 debuginfo(build-id) = 2cdb58c6e425be0b944bf91cbdd415d58f3dc8f6 debuginfo(build-id) = 36f20db829b7e4766b7dc29c1000303686a38b27 debuginfo(build-id) = 3e1ec4b8cb33a27f4397b4621bc7d33f8b969013 debuginfo(build-id) = 4a4662988d2aa3de26afc8a126949528704f092c debuginfo(build-id) = 609111d156a6df4b8a9cc2fec9e9f662fb89b5a1 debuginfo(build-id) = 655323f5d9f91586c7635414e89f2272c7c01724 debuginfo(build-id) = 655b7c7aa71f15104cd1d7da2611a08646704d4a debuginfo(build-id) = 6a3f52550a4cde06450073fc35c908b2ff0fc6bb debuginfo(build-id) = 7123fabba8f837a13061bcff97b725d44a868958 debuginfo(build-id) = 7748dd90f2505970fc4d3550890ea80952256895 debuginfo(build-id) = 78c0a804c033bc3868eb01384106ea165d2d4db2 debuginfo(build-id) = 7ec40702b604a682988de31be69c691348b9947c debuginfo(build-id) = 82bb1ddbb94b3d4633b13810903e5bba96bfea4b debuginfo(build-id) = 85f7dbef270b33b06c10e6ac38fe6597279c53f2 debuginfo(build-id) = 8e502470da92f9f9efd5e8dbe52601787b090ab3 debuginfo(build-id) = 984c8d32dfa7a7b3a14fd03d547557445387cae2 debuginfo(build-id) = 9cb8b4186fb2611f83e8a0e429a30e088e61e788 debuginfo(build-id) = a7399f1cc5898cfb8742f30dff0461f32b77cf5e debuginfo(build-id) = ac1ffae7dca3f93cac965bcf81b4166bfcf02114 debuginfo(build-id) = b033e02fc393f78410a48f3c7a5030e26b0d9425 debuginfo(build-id) = b2bf91a425da1c18710f791015bc662285d3acd5 debuginfo(build-id) = b3587e4815d1bbc139da0a6523787028b8b2997e debuginfo(build-id) = bbb30df94bf83971f2bde7d3b09ae949de8f50f0 debuginfo(build-id) = bd0122437a75ad5e3384206679341148d0f83356 debuginfo(build-id) = c23cfbfeb8803364d8692213e22559586db7a370 debuginfo(build-id) = cfa42b2d1ef4c65027d2c759e4b0ca1a12b31166 debuginfo(build-id) = da1f3bd8589f5227fe3b5adcb5459f746232cfd2 debuginfo(build-id) = dcc8cdc3010ab89ded3b2802f7d57c8a59e0b0f6 debuginfo(build-id) = de2d75d68bfec70417ff1715926fbee913b4b9df debuginfo(build-id) = e1c808357140ae5b2ff662f78fc061348480a9ef debuginfo(build-id) = e47041f698c2104a1c89556f633df11e79e6765b debuginfo(build-id) = ec16a4b1c28dbac92a5dadb7aaf20a96d340390d debuginfo(build-id) = edc5fe1b02eabe56137b653c65e9f773b0b4c826 debuginfo(build-id) = f53084f80f3115c589761acf2679b35ecc323492 debuginfo(build-id) = f7c887161121665ba7940465b2674f55e3317dc6 debuginfo(build-id) = f9f3e935d1597f36b6ad5b34c014e3d7c0d4046f debuginfo(build-id) = fe403f928b8ec866a4293a9a52529f3ab772d9e0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-64) = 1.23-1.el10 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64 Wrote: /builddir/build/RPMS/bcftools-1.23-1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.23-1.el10.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.23-1.el10.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.07xw8w + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.23 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.23-1.el10.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.8HZ3IK + 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-x86_64-1769509085.666809/root/var/log/dnf.rpm.log /var/lib/mock/centos-stream+epel-10-x86_64-1769509085.666809/root/var/log/dnf.librepo.log /var/lib/mock/centos-stream+epel-10-x86_64-1769509085.666809/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 20 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": "x86_64" }, { "name": "bcftools-debugsource", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "x86_64" }, { "name": "bcftools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "src" }, { "name": "bcftools", "epoch": null, "version": "1.23", "release": "1.el10", "arch": "x86_64" } ] } RPMResults finished