Warning: Permanently added '13.221.252.70' (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/10066101-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 1.6
PID: 9265
Logging PID: 9267
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 10066101,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': 'efa3fa6ff9b2446c154ce9c197ccbc3e2c0da4a6',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/samtools',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'samtools',
 'package_version': '1.23-1',
 'project_dirname': 'bioinformatics',
 'project_name': 'bioinformatics',
 'project_owner': 'ron',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/bioinformatics/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ron/bioinformatics--ron',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'ron',
 'tags': [],
 'task_id': '10066101-fedora-rawhide-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/samtools /var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/samtools', '/var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools'...

Running: git checkout efa3fa6ff9b2446c154ce9c197ccbc3e2c0da4a6 --

cmd: ['git', 'checkout', 'efa3fa6ff9b2446c154ce9c197ccbc3e2c0da4a6', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools
rc: 0
stdout: 
stderr: Note: switching to 'efa3fa6ff9b2446c154ce9c197ccbc3e2c0da4a6'.

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

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at efa3fa6 automatic import of samtools

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools
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 samtools-1.23.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o samtools-1.23.tar.bz2 --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ron/bioinformatics/samtools/samtools-1.23.tar.bz2/md5/7ce93103e5a3796c0009f879853837bb/samtools-1.23.tar.bz2
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 9138k  100 9138k    0     0  46.8M      0 --:--:-- --:--:-- --:--:-- 46.9M
INFO: Reading stdout from command: md5sum samtools-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-d1503i_u/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769501806.001017 -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-d1503i_u/samtools/samtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-d1503i_u/samtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769501806.001017 -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-d1503i_u/samtools/samtools.spec)  Config(fedora-rawhide-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/fedora-rawhide-x86_64-bootstrap-1769501806.001017/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: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Tagging container image as mock-bootstrap-701f9c99-c144-4821-b20a-8c6894f93bc6
INFO: Checking that b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 image matches host's architecture
INFO: Copy content of container b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1769501806.001017/root
INFO: mounting b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 with podman image mount
INFO: image b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 as /var/lib/containers/storage/overlay/eee5964c32f6db556d80a0c2d687049f5f34fc087d00ea1a2406a21ea4ce92a5/merged
INFO: umounting image b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 (/var/lib/containers/storage/overlay/eee5964c32f6db556d80a0c2d687049f5f34fc087d00ea1a2406a21ea4ce92a5/merged) with podman image umount
INFO: Removing image mock-bootstrap-701f9c99-c144-4821-b20a-8c6894f93bc6
INFO: Package manager dnf5 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/fedora-rawhide-x86_64-1769501806.001017/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 dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-6.0.1-2.fc44.x86_64
  rpm-sequoia-1.10.0-2.fc44.x86_64
  dnf5-5.3.0.0-7.fc44.x86_64
  dnf5-plugins-5.3.0.0-7.fc44.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 Copr repository                        100% |   4.1 KiB/s |   3.9 KiB |  00m01s
 fedora                                 100% |  14.8 MiB/s |  22.1 MiB |  00m01s
Repositories loaded.
Package                            Arch   Version                      Repository      Size
Installing group/module packages:
 bash                              x86_64 0:5.3.9-3.fc44               fedora       8.5 MiB
 bzip2                             x86_64 0:1.0.8-23.fc44              fedora      95.0 KiB
 coreutils                         x86_64 0:9.9-4.fc44                 fedora       5.4 MiB
 cpio                              x86_64 0:2.15-6.fc43                fedora       1.1 MiB
 diffutils                         x86_64 0:3.12-5.fc44                fedora       1.6 MiB
 fedora-release-common             noarch 0:44-0.10                    fedora      20.6 KiB
 findutils                         x86_64 1:4.10.0-7.fc44              fedora       1.9 MiB
 gawk                              x86_64 0:5.3.2-3.fc44               fedora       1.8 MiB
 glibc-minimal-langpack            x86_64 0:2.42.9000-25.fc44          fedora       0.0   B
 grep                              x86_64 0:3.12-3.fc44                fedora       1.0 MiB
 gzip                              x86_64 0:1.14-2.fc44                fedora     401.6 KiB
 info                              x86_64 0:7.2-7.fc44                 fedora     357.9 KiB
 patch                             x86_64 0:2.8-4.fc44                 fedora     226.6 KiB
 redhat-rpm-config                 noarch 0:343-19.fc44                fedora     183.6 KiB
 rpm-build                         x86_64 0:6.0.1-2.fc44               fedora     294.6 KiB
 sed                               x86_64 0:4.9-7.fc44                 fedora     857.2 KiB
 shadow-utils                      x86_64 2:4.18.0-7.fc44              fedora       3.9 MiB
 tar                               x86_64 2:1.35-8.fc44                fedora       3.0 MiB
 unzip                             x86_64 0:6.0-69.fc44                fedora     445.8 KiB
 util-linux                        x86_64 0:2.41.3-12.fc44             fedora       3.5 MiB
 which                             x86_64 0:2.23-4.fc44                fedora      83.4 KiB
 xz                                x86_64 1:5.8.2-2.fc44               fedora       1.3 MiB
Installing dependencies:
 R-srpm-macros                     noarch 0:1.3.4-3.fc44               fedora       3.4 KiB
 add-determinism                   x86_64 0:0.7.2-3.fc44               fedora       2.3 MiB
 alternatives                      x86_64 0:1.33-5.fc44                fedora      62.1 KiB
 ansible-srpm-macros               noarch 0:1-20.1.fc44                fedora      35.7 KiB
 audit-libs                        x86_64 0:4.1.2-4.fc44               fedora     390.5 KiB
 binutils                          x86_64 0:2.45.50-19.fc44            fedora      27.4 MiB
 build-reproducibility-srpm-macros noarch 0:0.7.2-3.fc44               fedora       1.2 KiB
 bzip2-libs                        x86_64 0:1.0.8-23.fc44              fedora      80.5 KiB
 ca-certificates                   noarch 0:2025.2.80_v9.0.304-5.fc44  fedora       2.7 MiB
 cmake-srpm-macros                 noarch 0:3.31.10-5.fc44             fedora     524.0   B
 coreutils-common                  x86_64 0:9.9-4.fc44                 fedora      11.2 MiB
 crypto-policies                   noarch 0:20251128-3.git19878fe.fc44 fedora     132.6 KiB
 curl                              x86_64 0:8.18.0-3.fc44              fedora     480.0 KiB
 cyrus-sasl-lib                    x86_64 0:2.1.28-35.fc44             fedora       2.3 MiB
 debugedit                         x86_64 0:5.2-6.fc44                 fedora     218.3 KiB
 dwz                               x86_64 0:0.16-3.fc44                fedora     290.9 KiB
 ed                                x86_64 0:1.22.4-2.fc44              fedora     149.1 KiB
 efi-srpm-macros                   noarch 0:6-6.fc44                   fedora      40.2 KiB
 elfutils                          x86_64 0:0.194-3.fc44               fedora       2.9 MiB
 elfutils-debuginfod-client        x86_64 0:0.194-3.fc44               fedora      83.7 KiB
 elfutils-default-yama-scope       noarch 0:0.194-3.fc44               fedora       1.8 KiB
 elfutils-libelf                   x86_64 0:0.194-3.fc44               fedora       1.1 MiB
 elfutils-libs                     x86_64 0:0.194-3.fc44               fedora     715.3 KiB
 fedora-gpg-keys                   noarch 0:44-0.1                     fedora     131.2 KiB
 fedora-release                    noarch 0:44-0.10                    fedora       0.0   B
 fedora-release-identity-basic     noarch 0:44-0.10                    fedora     664.0   B
 fedora-repos                      noarch 0:44-0.1                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch 0:44-0.1                     fedora       2.2 KiB
 file                              x86_64 0:5.46-9.fc44                fedora     100.1 KiB
 file-libs                         x86_64 0:5.46-9.fc44                fedora      11.9 MiB
 filesystem                        x86_64 0:3.18-52.fc44               fedora     112.0   B
 filesystem-srpm-macros            noarch 0:3.18-52.fc44               fedora      38.2 KiB
 fonts-srpm-macros                 noarch 1:5.0.0-2.fc44               fedora      55.8 KiB
 forge-srpm-macros                 noarch 0:0.4.0-4.fc44               fedora      38.9 KiB
 fpc-srpm-macros                   noarch 0:1.3-16.fc44                fedora     144.0   B
 gap-srpm-macros                   noarch 0:2-2.fc44                   fedora       2.1 KiB
 gdb-minimal                       x86_64 0:17.1-2.fc44                fedora      14.3 MiB
 gdbm-libs                         x86_64 1:1.23-11.fc44               fedora     129.6 KiB
 ghc-srpm-macros                   noarch 0:1.9.2-4.fc44               fedora     779.0   B
 glibc                             x86_64 0:2.42.9000-25.fc44          fedora       6.9 MiB
 glibc-common                      x86_64 0:2.42.9000-25.fc44          fedora       1.0 MiB
 glibc-gconv-extra                 x86_64 0:2.42.9000-25.fc44          fedora       7.4 MiB
 gmp                               x86_64 1:6.3.0-5.fc44               fedora     815.2 KiB
 gnat-srpm-macros                  noarch 0:7-2.fc44                   fedora       1.0 KiB
 gnulib-l10n                       noarch 0:20241231-2.fc44            fedora     655.0 KiB
 gnupg2                            x86_64 0:2.4.9-4.fc44               fedora       6.5 MiB
 gnupg2-dirmngr                    x86_64 0:2.4.9-4.fc44               fedora     634.0 KiB
 gnupg2-gpg-agent                  x86_64 0:2.4.9-4.fc44               fedora     682.5 KiB
 gnupg2-gpgconf                    x86_64 0:2.4.9-4.fc44               fedora     249.7 KiB
 gnupg2-keyboxd                    x86_64 0:2.4.9-4.fc44               fedora     201.2 KiB
 gnupg2-verify                     x86_64 0:2.4.9-4.fc44               fedora     360.3 KiB
 gnutls                            x86_64 0:3.8.11-10.fc44             fedora       3.7 MiB
 go-srpm-macros                    noarch 0:3.8.0-2.fc44               fedora      61.9 KiB
 gpgverify                         noarch 0:2.2-4.fc44                 fedora       8.7 KiB
 ima-evm-utils-libs                x86_64 0:1.6.2-8.fc44               fedora      60.6 KiB
 jansson                           x86_64 0:2.14-4.fc44                fedora      88.9 KiB
 java-srpm-macros                  noarch 0:1-8.fc44                   fedora     870.0   B
 json-c                            x86_64 0:0.18-8.fc44                fedora      82.6 KiB
 kernel-srpm-macros                noarch 0:1.0-28.fc44                fedora       1.9 KiB
 keyutils-libs                     x86_64 0:1.6.3-7.fc44               fedora      54.2 KiB
 krb5-libs                         x86_64 0:1.21.3-12.fc44             fedora       2.4 MiB
 libacl                            x86_64 0:2.3.2-6.fc44               fedora      35.8 KiB
 libarchive                        x86_64 0:3.8.4-2.fc44               fedora     991.2 KiB
 libassuan                         x86_64 0:2.5.7-5.fc44               fedora     163.8 KiB
 libattr                           x86_64 0:2.5.2-8.fc44               fedora      24.3 KiB
 libblkid                          x86_64 0:2.41.3-12.fc44             fedora     274.3 KiB
 libbrotli                         x86_64 0:1.2.0-3.fc44               fedora     865.0 KiB
 libcap                            x86_64 0:2.77-2.fc44                fedora     212.1 KiB
 libcap-ng                         x86_64 0:0.9-5.fc44                 fedora      68.7 KiB
 libcom_err                        x86_64 0:1.47.3-4.fc44              fedora      63.0 KiB
 libcurl                           x86_64 0:8.18.0-3.fc44              fedora       1.0 MiB
 libeconf                          x86_64 0:0.7.9-3.fc44               fedora      64.8 KiB
 libevent                          x86_64 0:2.1.12-17.fc44             fedora     978.7 KiB
 libfdisk                          x86_64 0:2.41.3-12.fc44             fedora     388.3 KiB
 libffi                            x86_64 0:3.5.2-2.fc44               fedora      87.7 KiB
 libfsverity                       x86_64 0:1.6-4.fc44                 fedora      28.4 KiB
 libgcc                            x86_64 0:16.0.1-0.3.fc44.1          fedora     270.6 KiB
 libgcrypt                         x86_64 0:1.11.2-1.fc44              fedora       1.6 MiB
 libgomp                           x86_64 0:16.0.1-0.3.fc44.1          fedora     571.5 KiB
 libgpg-error                      x86_64 0:1.58-2.fc44                fedora     941.6 KiB
 libidn2                           x86_64 0:2.3.8-3.fc44               fedora     556.4 KiB
 libksba                           x86_64 0:1.6.7-5.fc44               fedora     414.4 KiB
 liblastlog2                       x86_64 0:2.41.3-12.fc44             fedora      37.6 KiB
 libmount                          x86_64 0:2.41.3-12.fc44             fedora     388.6 KiB
 libnghttp2                        x86_64 0:1.68.0-3.fc44              fedora     166.1 KiB
 libnghttp3                        x86_64 0:1.15.0-1.fc44              fedora     159.2 KiB
 libpkgconf                        x86_64 0:2.3.0-4.fc44               fedora      78.0 KiB
 libpsl                            x86_64 0:0.21.5-7.fc44              fedora      76.3 KiB
 libselinux                        x86_64 0:3.9-7.fc44                 fedora     201.0 KiB
 libselinux-utils                  x86_64 0:3.9-7.fc44                 fedora     305.7 KiB
 libsemanage                       x86_64 0:3.9-5.fc44                 fedora     312.3 KiB
 libsepol                          x86_64 0:3.9-3.fc44                 fedora     861.8 KiB
 libsmartcols                      x86_64 0:2.41.3-12.fc44             fedora     188.3 KiB
 libssh                            x86_64 0:0.11.3-1.fc44              fedora     567.1 KiB
 libssh-config                     noarch 0:0.11.3-1.fc44              fedora     277.0   B
 libstdc++                         x86_64 0:16.0.1-0.3.fc44.1          fedora       2.9 MiB
 libtasn1                          x86_64 0:4.20.0-3.fc44              fedora     180.2 KiB
 libtool-ltdl                      x86_64 0:2.5.4-10.fc44              fedora      70.0 KiB
 libunistring                      x86_64 0:1.1-11.fc44                fedora       1.7 MiB
 libusb1                           x86_64 0:1.0.29-5.fc44              fedora     175.2 KiB
 libuuid                           x86_64 0:2.41.3-12.fc44             fedora      37.2 KiB
 libverto                          x86_64 0:0.3.2-12.fc44              fedora      25.3 KiB
 libxcrypt                         x86_64 0:4.5.2-3.fc44               fedora     293.2 KiB
 libxml2                           x86_64 0:2.12.10-6.fc44             fedora       1.8 MiB
 libzstd                           x86_64 0:1.5.7-5.fc44               fedora     956.1 KiB
 linkdupes                         x86_64 0:0.7.2-3.fc44               fedora     826.6 KiB
 lua-libs                          x86_64 0:5.4.8-5.fc44               fedora     281.7 KiB
 lua-srpm-macros                   noarch 0:1-17.fc44                  fedora       1.3 KiB
 lz4-libs                          x86_64 0:1.10.0-4.fc44              fedora     157.3 KiB
 mpfr                              x86_64 0:4.2.2-3.fc44               fedora     849.1 KiB
 ncurses-base                      noarch 0:6.5-9.20250614.fc44        fedora     328.1 KiB
 ncurses-libs                      x86_64 0:6.5-9.20250614.fc44        fedora     965.0 KiB
 nettle                            x86_64 0:3.10.1-3.fc44              fedora     794.3 KiB
 ngtcp2                            x86_64 0:1.19.0-2.fc44              fedora     330.2 KiB
 ngtcp2-crypto-ossl                x86_64 0:1.19.0-2.fc44              fedora      51.6 KiB
 npth                              x86_64 0:1.8-4.fc44                 fedora      49.5 KiB
 ocaml-srpm-macros                 noarch 0:11-3.fc44                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 0:2-21.fc44                  fedora     112.0   B
 openldap                          x86_64 0:2.6.10-7.fc44              fedora     667.5 KiB
 openssl-libs                      x86_64 1:3.5.4-2.fc44               fedora       9.2 MiB
 p11-kit                           x86_64 0:0.25.8-2.fc44              fedora       2.3 MiB
 p11-kit-trust                     x86_64 0:0.25.8-2.fc44              fedora     458.3 KiB
 package-notes-srpm-macros         noarch 0:0.5-15.fc44                fedora       1.6 KiB
 pam-libs                          x86_64 0:1.7.2-1.fc44               fedora     130.5 KiB
 pcre2                             x86_64 0:10.47-1.fc44.1             fedora     718.6 KiB
 pcre2-syntax                      noarch 0:10.47-1.fc44.1             fedora     281.9 KiB
 perl-srpm-macros                  noarch 0:1-61.fc44                  fedora     861.0   B
 pkgconf                           x86_64 0:2.3.0-4.fc44               fedora      88.3 KiB
 pkgconf-m4                        noarch 0:2.3.0-4.fc44               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 0:2.3.0-4.fc44               fedora     989.0   B
 policycoreutils                   x86_64 0:3.9-8.fc44                 fedora     883.8 KiB
 popt                              x86_64 0:1.19-10.fc44               fedora     132.6 KiB
 publicsuffix-list-dafsa           noarch 0:20260116-1.fc44            fedora      70.4 KiB
 pyproject-srpm-macros             noarch 0:1.18.6-2.fc44              fedora       1.9 KiB
 python-srpm-macros                noarch 0:3.14-10.fc44               fedora      51.6 KiB
 qt5-srpm-macros                   noarch 0:5.15.18-2.fc44             fedora     500.0   B
 qt6-srpm-macros                   noarch 0:6.10.1-2.fc44              fedora     464.0   B
 readline                          x86_64 0:8.3-4.fc44                 fedora     519.5 KiB
 rpm                               x86_64 0:6.0.1-2.fc44               fedora       3.1 MiB
 rpm-build-libs                    x86_64 0:6.0.1-2.fc44               fedora     276.3 KiB
 rpm-libs                          x86_64 0:6.0.1-2.fc44               fedora     961.2 KiB
 rpm-plugin-selinux                x86_64 0:6.0.1-2.fc44               fedora      11.9 KiB
 rpm-sequoia                       x86_64 0:1.10.0-2.fc44              fedora       2.5 MiB
 rpm-sign-libs                     x86_64 0:6.0.1-2.fc44               fedora      39.6 KiB
 rust-srpm-macros                  noarch 0:28.4-3.fc44                fedora       5.5 KiB
 selinux-policy                    noarch 0:42.22-1.fc44               fedora      32.0 KiB
 selinux-policy-targeted           noarch 0:42.22-1.fc44               fedora      18.5 MiB
 setup                             noarch 0:2.15.0-28.fc44             fedora     724.9 KiB
 sqlite-libs                       x86_64 0:3.51.2-1.fc44              fedora       1.6 MiB
 systemd-libs                      x86_64 0:259-9.fc44                 fedora       2.4 MiB
 systemd-standalone-sysusers       x86_64 0:259-9.fc44                 fedora     301.6 KiB
 tpm2-tss                          x86_64 0:4.1.3-9.fc44               fedora       1.6 MiB
 tree-sitter-srpm-macros           noarch 0:0.4.2-2.fc44               fedora       8.3 KiB
 util-linux-core                   x86_64 0:2.41.3-12.fc44             fedora       1.5 MiB
 xxhash-libs                       x86_64 0:0.8.3-4.fc44               fedora      94.0 KiB
 xz-libs                           x86_64 1:5.8.2-2.fc44               fedora     217.7 KiB
 zig-srpm-macros                   noarch 0:1-8.fc44                   fedora       1.3 KiB
 zip                               x86_64 0:3.0-45.fc44                fedora     698.0 KiB
 zlib-ng-compat                    x86_64 0:2.3.2-3.fc44               fedora     169.6 KiB
 zstd                              x86_64 0:1.5.7-5.fc44               fedora     502.4 KiB
Installing groups:
 Buildsystem building group                                                                

Transaction Summary:
 Installing:       182 packages

Total size of inbound packages is 68 MiB. Need to download 68 MiB.
After this operation, 223 MiB extra will be used (install 223 MiB, remove 0 B).
[  1/182] bzip2-0:1.0.8-23.fc44.x86_64  100% | 668.1 KiB/s |  52.1 KiB |  00m00s
[  2/182] cpio-0:2.15-6.fc43.x86_64     100% |   3.6 MiB/s | 293.1 KiB |  00m00s
[  3/182] bash-0:5.3.9-3.fc44.x86_64    100% |   9.4 MiB/s |   1.9 MiB |  00m00s
[  4/182] coreutils-0:9.9-4.fc44.x86_64 100% |   5.6 MiB/s |   1.2 MiB |  00m00s
[  5/182] diffutils-0:3.12-5.fc44.x86_6 100% |   3.6 MiB/s | 395.3 KiB |  00m00s
[  6/182] fedora-release-common-0:44-0. 100% | 237.2 KiB/s |  24.7 KiB |  00m00s
[  7/182] findutils-1:4.10.0-7.fc44.x86 100% |   4.7 MiB/s | 552.5 KiB |  00m00s
[  8/182] grep-0:3.12-3.fc44.x86_64     100% |   2.1 MiB/s | 301.6 KiB |  00m00s
[  9/182] info-0:7.2-7.fc44.x86_64      100% |   2.3 MiB/s | 182.9 KiB |  00m00s
[ 10/182] glibc-minimal-langpack-0:2.42 100% | 289.3 KiB/s |  76.9 KiB |  00m00s
[ 11/182] patch-0:2.8-4.fc44.x86_64     100% |   7.0 MiB/s | 115.2 KiB |  00m00s
[ 12/182] gzip-0:1.14-2.fc44.x86_64     100% | 755.6 KiB/s | 179.1 KiB |  00m00s
[ 13/182] rpm-build-0:6.0.1-2.fc44.x86_ 100% |   3.5 MiB/s | 139.9 KiB |  00m00s
[ 14/182] redhat-rpm-config-0:343-19.fc 100% |   1.1 MiB/s |  79.4 KiB |  00m00s
[ 15/182] sed-0:4.9-7.fc44.x86_64       100% |   3.1 MiB/s | 319.2 KiB |  00m00s
[ 16/182] shadow-utils-2:4.18.0-7.fc44. 100% |  13.6 MiB/s |   1.3 MiB |  00m00s
[ 17/182] which-0:2.23-4.fc44.x86_64    100% |   1.8 MiB/s |  42.2 KiB |  00m00s
[ 18/182] tar-2:1.35-8.fc44.x86_64      100% |   6.8 MiB/s | 868.2 KiB |  00m00s
[ 19/182] xz-1:5.8.2-2.fc44.x86_64      100% |   8.5 MiB/s | 607.2 KiB |  00m00s
[ 20/182] unzip-0:6.0-69.fc44.x86_64    100% |   1.3 MiB/s | 199.6 KiB |  00m00s
[ 21/182] gawk-0:5.3.2-3.fc44.x86_64    100% |   4.8 MiB/s |   1.1 MiB |  00m00s
[ 22/182] util-linux-0:2.41.3-12.fc44.x 100% |   6.1 MiB/s |   1.2 MiB |  00m00s
[ 23/182] ncurses-libs-0:6.5-9.20250614 100% |   3.2 MiB/s | 343.1 KiB |  00m00s
[ 24/182] bzip2-libs-0:1.0.8-23.fc44.x8 100% |   1.8 MiB/s |  43.8 KiB |  00m00s
[ 25/182] filesystem-0:3.18-52.fc44.x86 100% |   4.2 MiB/s |   1.3 MiB |  00m00s
[ 26/182] gmp-1:6.3.0-5.fc44.x86_64     100% |   1.8 MiB/s | 322.5 KiB |  00m00s
[ 27/182] glibc-0:2.42.9000-25.fc44.x86 100% |   6.8 MiB/s |   2.4 MiB |  00m00s
[ 28/182] coreutils-common-0:9.9-4.fc44 100% |   7.7 MiB/s |   2.1 MiB |  00m00s
[ 29/182] libacl-0:2.3.2-6.fc44.x86_64  100% | 164.4 KiB/s |  24.8 KiB |  00m00s
[ 30/182] libattr-0:2.5.2-8.fc44.x86_64 100% | 112.8 KiB/s |  17.9 KiB |  00m00s
[ 31/182] libcap-0:2.77-2.fc44.x86_64   100% | 646.2 KiB/s |  88.5 KiB |  00m00s
[ 32/182] libselinux-0:3.9-7.fc44.x86_6 100% | 752.5 KiB/s | 101.6 KiB |  00m00s
[ 33/182] systemd-libs-0:259-9.fc44.x86 100% |   6.2 MiB/s | 865.2 KiB |  00m00s
[ 34/182] glibc-common-0:2.42.9000-25.f 100% |  10.6 MiB/s | 368.9 KiB |  00m00s
[ 35/182] pcre2-0:10.47-1.fc44.1.x86_64 100% |   6.8 MiB/s | 277.7 KiB |  00m00s
[ 36/182] ed-0:1.22.4-2.fc44.x86_64     100% |   6.0 MiB/s |  85.6 KiB |  00m00s
[ 37/182] R-srpm-macros-0:1.3.4-3.fc44. 100% | 636.4 KiB/s |  10.8 KiB |  00m00s
[ 38/182] ansible-srpm-macros-0:1-20.1. 100% |   1.2 MiB/s |  20.1 KiB |  00m00s
[ 39/182] build-reproducibility-srpm-ma 100% |   1.2 MiB/s |  13.0 KiB |  00m00s
[ 40/182] cmake-srpm-macros-0:3.31.10-5 100% | 343.3 KiB/s |  10.6 KiB |  00m00s
[ 41/182] dwz-0:0.16-3.fc44.x86_64      100% |   2.2 MiB/s | 138.9 KiB |  00m00s
[ 42/182] efi-srpm-macros-0:6-6.fc44.no 100% |   1.4 MiB/s |  22.6 KiB |  00m00s
[ 43/182] file-0:5.46-9.fc44.x86_64     100% |   1.5 MiB/s |  49.0 KiB |  00m00s
[ 44/182] filesystem-srpm-macros-0:3.18 100% |   2.0 MiB/s |  26.6 KiB |  00m00s
[ 45/182] openssl-libs-1:3.5.4-2.fc44.x 100% |   5.5 MiB/s |   2.7 MiB |  00m01s
[ 46/182] fonts-srpm-macros-1:5.0.0-2.f 100% | 883.3 KiB/s |  27.4 KiB |  00m00s
[ 47/182] fpc-srpm-macros-0:1.3-16.fc44 100% | 793.8 KiB/s |   7.9 KiB |  00m00s
[ 48/182] gap-srpm-macros-0:2-2.fc44.no 100% | 507.8 KiB/s |   9.1 KiB |  00m00s
[ 49/182] fedora-repos-0:44-0.1.noarch  100% |  20.5 KiB/s |   9.1 KiB |  00m00s
[ 50/182] ghc-srpm-macros-0:1.9.2-4.fc4 100% | 121.6 KiB/s |   8.9 KiB |  00m00s
[ 51/182] go-srpm-macros-0:3.8.0-2.fc44 100% | 600.5 KiB/s |  28.2 KiB |  00m00s
[ 52/182] java-srpm-macros-0:1-8.fc44.n 100% | 219.3 KiB/s |   8.1 KiB |  00m00s
[ 53/182] kernel-srpm-macros-0:1.0-28.f 100% | 603.1 KiB/s |   9.0 KiB |  00m00s
[ 54/182] forge-srpm-macros-0:0.4.0-4.f 100% |  85.0 KiB/s |  20.0 KiB |  00m00s
[ 55/182] lua-srpm-macros-0:1-17.fc44.n 100% | 261.1 KiB/s |   8.9 KiB |  00m00s
[ 56/182] gnat-srpm-macros-0:7-2.fc44.n 100% |  45.1 KiB/s |   8.7 KiB |  00m00s
[ 57/182] openblas-srpm-macros-0:2-21.f 100% | 300.2 KiB/s |   7.8 KiB |  00m00s
[ 58/182] perl-srpm-macros-0:1-61.fc44. 100% |   1.0 MiB/s |   8.4 KiB |  00m00s
[ 59/182] pyproject-srpm-macros-0:1.18. 100% | 614.5 KiB/s |  13.5 KiB |  00m00s
[ 60/182] python-srpm-macros-0:3.14-10. 100% |   1.1 MiB/s |  24.0 KiB |  00m00s
[ 61/182] qt5-srpm-macros-0:5.15.18-2.f 100% | 222.8 KiB/s |   8.7 KiB |  00m00s
[ 62/182] ocaml-srpm-macros-0:11-3.fc44 100% |  51.2 KiB/s |   9.3 KiB |  00m00s
[ 63/182] qt6-srpm-macros-0:6.10.1-2.fc 100% | 162.2 KiB/s |   9.2 KiB |  00m00s
[ 64/182] package-notes-srpm-macros-0:0 100% |  52.8 KiB/s |   9.2 KiB |  00m00s
[ 65/182] rust-srpm-macros-0:28.4-3.fc4 100% | 235.4 KiB/s |  11.1 KiB |  00m00s
[ 66/182] rpm-0:6.0.1-2.fc44.x86_64     100% |   4.1 MiB/s | 578.3 KiB |  00m00s
[ 67/182] tree-sitter-srpm-macros-0:0.4 100% |  94.9 KiB/s |  13.5 KiB |  00m00s
[ 68/182] zig-srpm-macros-0:1-8.fc44.no 100% |  69.4 KiB/s |   8.8 KiB |  00m00s
[ 69/182] zip-0:3.0-45.fc44.x86_64      100% |   2.6 MiB/s | 264.4 KiB |  00m00s
[ 70/182] elfutils-0:0.194-3.fc44.x86_6 100% |   6.0 MiB/s | 583.9 KiB |  00m00s
[ 71/182] debugedit-0:5.2-6.fc44.x86_64 100% | 652.0 KiB/s |  86.7 KiB |  00m00s
[ 72/182] libarchive-0:3.8.4-2.fc44.x86 100% |   7.6 MiB/s | 441.4 KiB |  00m00s
[ 73/182] elfutils-libelf-0:0.194-3.fc4 100% |   1.9 MiB/s | 205.1 KiB |  00m00s
[ 74/182] libgcc-0:16.0.1-0.3.fc44.1.x8 100% |   1.4 MiB/s | 115.4 KiB |  00m00s
[ 75/182] popt-0:1.19-10.fc44.x86_64    100% | 485.0 KiB/s |  66.9 KiB |  00m00s
[ 76/182] libstdc++-0:16.0.1-0.3.fc44.1 100% |   4.7 MiB/s | 937.9 KiB |  00m00s
[ 77/182] readline-0:8.3-4.fc44.x86_64  100% |   1.2 MiB/s | 229.8 KiB |  00m00s
[ 78/182] rpm-build-libs-0:6.0.1-2.fc44 100% | 887.2 KiB/s | 132.2 KiB |  00m00s
[ 79/182] rpm-libs-0:6.0.1-2.fc44.x86_6 100% |   3.1 MiB/s | 415.5 KiB |  00m00s
[ 80/182] zstd-0:1.5.7-5.fc44.x86_64    100% |   1.3 MiB/s | 192.5 KiB |  00m00s
[ 81/182] audit-libs-0:4.1.2-4.fc44.x86 100% |   1.2 MiB/s | 141.3 KiB |  00m00s
[ 82/182] libeconf-0:0.7.9-3.fc44.x86_6 100% | 309.5 KiB/s |  36.2 KiB |  00m00s
[ 83/182] pam-libs-0:1.7.2-1.fc44.x86_6 100% |   2.5 MiB/s |  59.1 KiB |  00m00s
[ 84/182] libsemanage-0:3.9-5.fc44.x86_ 100% |   1.2 MiB/s | 126.6 KiB |  00m00s
[ 85/182] libxcrypt-0:4.5.2-3.fc44.x86_ 100% |   1.4 MiB/s | 131.2 KiB |  00m00s
[ 86/182] setup-0:2.15.0-28.fc44.noarch 100% |   2.3 MiB/s | 157.2 KiB |  00m00s
[ 87/182] libblkid-0:2.41.3-12.fc44.x86 100% |   2.1 MiB/s | 129.4 KiB |  00m00s
[ 88/182] xz-libs-1:5.8.2-2.fc44.x86_64 100% | 744.1 KiB/s | 116.8 KiB |  00m00s
[ 89/182] libcap-ng-0:0.9-5.fc44.x86_64 100% | 695.6 KiB/s |  32.7 KiB |  00m00s
[ 90/182] liblastlog2-0:2.41.3-12.fc44. 100% | 782.0 KiB/s |  23.5 KiB |  00m00s
[ 91/182] mpfr-0:4.2.2-3.fc44.x86_64    100% |   2.1 MiB/s | 357.8 KiB |  00m00s
[ 92/182] libmount-0:2.41.3-12.fc44.x86 100% |   9.8 MiB/s | 171.0 KiB |  00m00s
[ 93/182] libuuid-0:2.41.3-12.fc44.x86_ 100% |   1.3 MiB/s |  26.6 KiB |  00m00s
[ 94/182] libfdisk-0:2.41.3-12.fc44.x86 100% |   1.8 MiB/s | 168.1 KiB |  00m00s
[ 95/182] libsmartcols-0:2.41.3-12.fc44 100% | 987.8 KiB/s |  86.9 KiB |  00m00s
[ 96/182] util-linux-core-0:2.41.3-12.f 100% |   6.8 MiB/s | 557.8 KiB |  00m00s
[ 97/182] zlib-ng-compat-0:2.3.2-3.fc44 100% |   1.3 MiB/s |  93.0 KiB |  00m00s
[ 98/182] glibc-gconv-extra-0:2.42.9000 100% |  10.5 MiB/s |   1.6 MiB |  00m00s
[ 99/182] ncurses-base-0:6.5-9.20250614 100% | 447.6 KiB/s |  88.2 KiB |  00m00s
[100/182] gnulib-l10n-0:20241231-2.fc44 100% | 686.4 KiB/s | 150.3 KiB |  00m00s
[101/182] libsepol-0:3.9-3.fc44.x86_64  100% |   2.1 MiB/s | 362.9 KiB |  00m00s
[102/182] crypto-policies-0:20251128-3. 100% | 910.2 KiB/s |  98.3 KiB |  00m00s
[103/182] ca-certificates-0:2025.2.80_v 100% |   7.0 MiB/s | 973.5 KiB |  00m00s
[104/182] pcre2-syntax-0:10.47-1.fc44.1 100% |   9.5 MiB/s | 164.7 KiB |  00m00s
[105/182] fedora-gpg-keys-0:44-0.1.noar 100% |   1.3 MiB/s | 138.8 KiB |  00m00s
[106/182] fedora-repos-rawhide-0:44-0.1 100% |  90.1 KiB/s |   8.6 KiB |  00m00s
[107/182] add-determinism-0:0.7.2-3.fc4 100% |   9.2 MiB/s | 881.3 KiB |  00m00s
[108/182] linkdupes-0:0.7.2-3.fc44.x86_ 100% |   3.5 MiB/s | 355.1 KiB |  00m00s
[109/182] curl-0:8.18.0-3.fc44.x86_64   100% |   3.6 MiB/s | 241.1 KiB |  00m00s
[110/182] elfutils-debuginfod-client-0: 100% |   2.7 MiB/s |  46.7 KiB |  00m00s
[111/182] file-libs-0:5.46-9.fc44.x86_6 100% |   4.4 MiB/s | 853.4 KiB |  00m00s
[112/182] elfutils-libs-0:0.194-3.fc44. 100% |   1.6 MiB/s | 282.8 KiB |  00m00s
[113/182] libzstd-0:1.5.7-5.fc44.x86_64 100% |   1.5 MiB/s | 364.2 KiB |  00m00s
[114/182] libgomp-0:16.0.1-0.3.fc44.1.x 100% |  11.1 MiB/s | 374.2 KiB |  00m00s
[115/182] lua-libs-0:5.4.8-5.fc44.x86_6 100% |   3.8 MiB/s | 136.6 KiB |  00m00s
[116/182] libxml2-0:2.12.10-6.fc44.x86_ 100% |   2.9 MiB/s | 724.6 KiB |  00m00s
[117/182] rpm-sign-libs-0:6.0.1-2.fc44. 100% | 801.1 KiB/s |  28.0 KiB |  00m00s
[118/182] lz4-libs-0:1.10.0-4.fc44.x86_ 100% | 366.5 KiB/s |  77.7 KiB |  00m00s
[119/182] rpm-sequoia-0:1.10.0-2.fc44.x 100% |   6.3 MiB/s | 939.7 KiB |  00m00s
[120/182] elfutils-default-yama-scope-0 100% |  88.9 KiB/s |  11.9 KiB |  00m00s
[121/182] sqlite-libs-0:3.51.2-1.fc44.x 100% |   4.0 MiB/s | 799.2 KiB |  00m00s
[122/182] json-c-0:0.18-8.fc44.x86_64   100% | 723.9 KiB/s |  46.3 KiB |  00m00s
[123/182] gnupg2-0:2.4.9-4.fc44.x86_64  100% |  12.2 MiB/s |   1.7 MiB |  00m00s
[124/182] ima-evm-utils-libs-0:1.6.2-8. 100% | 209.5 KiB/s |  30.0 KiB |  00m00s
[125/182] gnupg2-dirmngr-0:2.4.9-4.fc44 100% |   5.4 MiB/s | 282.5 KiB |  00m00s
[126/182] gnupg2-gpg-agent-0:2.4.9-4.fc 100% |   5.1 MiB/s | 281.4 KiB |  00m00s
[127/182] libfsverity-0:1.6-4.fc44.x86_ 100% |  65.9 KiB/s |  19.2 KiB |  00m00s
[128/182] gnupg2-gpgconf-0:2.4.9-4.fc44 100% |   1.5 MiB/s | 117.2 KiB |  00m00s
[129/182] gpgverify-0:2.2-4.fc44.noarch 100% |  45.6 KiB/s |  11.2 KiB |  00m00s
[130/182] gnupg2-keyboxd-0:2.4.9-4.fc44 100% |   1.4 MiB/s |  97.4 KiB |  00m00s
[131/182] gnupg2-verify-0:2.4.9-4.fc44. 100% |   3.0 MiB/s | 176.9 KiB |  00m00s
[132/182] libgpg-error-0:1.58-2.fc44.x8 100% |  12.4 MiB/s | 254.1 KiB |  00m00s
[133/182] npth-0:1.8-4.fc44.x86_64      100% |   1.1 MiB/s |  25.8 KiB |  00m00s
[134/182] tpm2-tss-0:4.1.3-9.fc44.x86_6 100% |  12.7 MiB/s | 440.9 KiB |  00m00s
[135/182] gnutls-0:3.8.11-10.fc44.x86_6 100% |  25.5 MiB/s |   1.4 MiB |  00m00s
[136/182] libksba-0:1.6.7-5.fc44.x86_64 100% |   4.7 MiB/s | 167.4 KiB |  00m00s
[137/182] libassuan-0:2.5.7-5.fc44.x86_ 100% | 274.4 KiB/s |  68.9 KiB |  00m00s
[138/182] openldap-0:2.6.10-7.fc44.x86_ 100% |   4.9 MiB/s | 271.1 KiB |  00m00s
[139/182] libidn2-0:2.3.8-3.fc44.x86_64 100% |   7.5 MiB/s | 175.6 KiB |  00m00s
[140/182] libgcrypt-0:1.11.2-1.fc44.x86 100% |   2.1 MiB/s | 596.1 KiB |  00m00s
[141/182] libusb1-0:1.0.29-5.fc44.x86_6 100% | 951.1 KiB/s |  82.8 KiB |  00m00s
[142/182] libtasn1-0:4.20.0-3.fc44.x86_ 100% | 501.0 KiB/s |  76.2 KiB |  00m00s
[143/182] p11-kit-0:0.25.8-2.fc44.x86_6 100% |   8.1 MiB/s | 516.5 KiB |  00m00s
[144/182] libunistring-0:1.1-11.fc44.x8 100% |   2.3 MiB/s | 547.8 KiB |  00m00s
[145/182] nettle-0:3.10.1-3.fc44.x86_64 100% |   1.8 MiB/s | 428.0 KiB |  00m00s
[146/182] cyrus-sasl-lib-0:2.1.28-35.fc 100% |   7.9 MiB/s | 800.7 KiB |  00m00s
[147/182] libevent-0:2.1.12-17.fc44.x86 100% |   3.1 MiB/s | 287.4 KiB |  00m00s
[148/182] libffi-0:3.5.2-2.fc44.x86_64  100% |   1.1 MiB/s |  42.4 KiB |  00m00s
[149/182] libtool-ltdl-0:2.5.4-10.fc44. 100% | 435.7 KiB/s |  37.0 KiB |  00m00s
[150/182] gdbm-libs-1:1.23-11.fc44.x86_ 100% | 708.5 KiB/s |  58.8 KiB |  00m00s
[151/182] alternatives-0:1.33-5.fc44.x8 100% | 628.4 KiB/s |  40.8 KiB |  00m00s
[152/182] jansson-0:2.14-4.fc44.x86_64  100% | 574.6 KiB/s |  47.1 KiB |  00m00s
[153/182] binutils-0:2.45.50-19.fc44.x8 100% |  39.8 MiB/s |   6.1 MiB |  00m00s
[154/182] pkgconf-pkg-config-0:2.3.0-4. 100% |  74.3 KiB/s |   9.7 KiB |  00m00s
[155/182] pkgconf-0:2.3.0-4.fc44.x86_64 100% | 478.5 KiB/s |  45.0 KiB |  00m00s
[156/182] libpkgconf-0:2.3.0-4.fc44.x86 100% | 881.4 KiB/s |  38.8 KiB |  00m00s
[157/182] p11-kit-trust-0:0.25.8-2.fc44 100% |   2.9 MiB/s | 144.8 KiB |  00m00s
[158/182] pkgconf-m4-0:2.3.0-4.fc44.noa 100% |  85.7 KiB/s |  14.1 KiB |  00m00s
[159/182] fedora-release-0:44-0.10.noar 100% | 214.4 KiB/s |  13.5 KiB |  00m00s
[160/182] systemd-standalone-sysusers-0 100% |   1.9 MiB/s | 148.3 KiB |  00m00s
[161/182] xxhash-libs-0:0.8.3-4.fc44.x8 100% | 549.6 KiB/s |  41.2 KiB |  00m00s
[162/182] fedora-release-identity-basic 100% | 216.3 KiB/s |  14.3 KiB |  00m00s
[163/182] gdb-minimal-0:17.1-2.fc44.x86 100% |  31.9 MiB/s |   4.8 MiB |  00m00s
[164/182] libbrotli-0:1.2.0-3.fc44.x86_ 100% |  11.7 MiB/s | 347.8 KiB |  00m00s
[165/182] libcurl-0:8.18.0-3.fc44.x86_6 100% |   4.4 MiB/s | 455.1 KiB |  00m00s
[166/182] libnghttp2-0:1.68.0-3.fc44.x8 100% |   1.4 MiB/s |  77.2 KiB |  00m00s
[167/182] libpsl-0:0.21.5-7.fc44.x86_64 100% |   3.7 MiB/s |  65.3 KiB |  00m00s
[168/182] krb5-libs-0:1.21.3-12.fc44.x8 100% |   4.6 MiB/s | 793.5 KiB |  00m00s
[169/182] libnghttp3-0:1.15.0-1.fc44.x8 100% | 642.9 KiB/s |  73.9 KiB |  00m00s
[170/182] libssh-0:0.11.3-1.fc44.x86_64 100% |   4.6 MiB/s | 232.8 KiB |  00m00s
[171/182] ngtcp2-0:1.19.0-2.fc44.x86_64 100% |   2.3 MiB/s | 154.8 KiB |  00m00s
[172/182] keyutils-libs-0:1.6.3-7.fc44. 100% | 630.6 KiB/s |  31.5 KiB |  00m00s
[173/182] ngtcp2-crypto-ossl-0:1.19.0-2 100% | 369.9 KiB/s |  27.4 KiB |  00m00s
[174/182] libverto-0:0.3.2-12.fc44.x86_ 100% | 812.5 KiB/s |  21.1 KiB |  00m00s
[175/182] libssh-config-0:0.11.3-1.fc44 100% | 759.3 KiB/s |   9.1 KiB |  00m00s
[176/182] libcom_err-0:1.47.3-4.fc44.x8 100% | 371.3 KiB/s |  27.1 KiB |  00m00s
[177/182] publicsuffix-list-dafsa-0:202 100% | 927.3 KiB/s |  60.3 KiB |  00m00s
[178/182] policycoreutils-0:3.9-8.fc44. 100% |   4.3 MiB/s | 258.6 KiB |  00m00s
[179/182] selinux-policy-targeted-0:42. 100% |  54.5 MiB/s |   6.8 MiB |  00m00s
[180/182] selinux-policy-0:42.22-1.fc44 100% | 837.2 KiB/s |  67.8 KiB |  00m00s
[181/182] rpm-plugin-selinux-0:6.0.1-2. 100% | 563.5 KiB/s |  19.2 KiB |  00m00s
[182/182] libselinux-utils-0:3.9-7.fc44 100% |   1.4 MiB/s | 119.7 KiB |  00m00s
--------------------------------------------------------------------------------
[182/182] Total                         100% |  10.6 MiB/s |  68.5 MiB |  00m06s
Running transaction
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
Importing OpenPGP key 0xF577861E:
 UserID     : "Fedora (45) <fedora-45-primary@fedoraproject.org>"
 Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary
The key was successfully imported.
[  1/184] Verify package files          100% | 716.0   B/s | 182.0   B |  00m00s
[  2/184] Prepare transaction           100% |   3.6 KiB/s | 182.0   B |  00m00s
[  3/184] Installing libgcc-0:16.0.1-0. 100% | 266.0 MiB/s | 272.3 KiB |  00m00s
[  4/184] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/184] Installing publicsuffix-list- 100% |   0.0   B/s |  71.1 KiB |  00m00s
[  6/184] Installing fedora-release-ide 100% |   0.0   B/s | 920.0   B |  00m00s
[  7/184] Installing fedora-gpg-keys-0: 100% |  43.7 MiB/s | 179.0 KiB |  00m00s
[  8/184] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  9/184] Installing fedora-repos-0:44- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/184] Installing fedora-release-com 100% |  24.3 MiB/s |  24.9 KiB |  00m00s
[ 11/184] Installing fedora-release-0:4 100% |  17.3 KiB/s | 124.0   B |  00m00s
>>> Running sysusers scriptlet: setup-0:2.15.0-28.fc44.noarch
>>> Finished sysusers scriptlet: setup-0:2.15.0-28.fc44.noarch
>>> Scriptlet output:
>>> Creating group 'adm' with GID 4.
>>> Creating group 'audio' with GID 63.
>>> Creating group 'cdrom' with GID 11.
>>> Creating group 'clock' with GID 103.
>>> Creating group 'dialout' with GID 18.
>>> Creating group 'disk' with GID 6.
>>> Creating group 'floppy' with GID 19.
>>> Creating group 'ftp' with GID 50.
>>> Creating group 'games' with GID 20.
>>> Creating group 'input' with GID 104.
>>> Creating group 'kmem' with GID 9.
>>> Creating group 'kvm' with GID 36.
>>> Creating group 'lock' with GID 54.
>>> Creating group 'lp' with GID 7.
>>> Creating group 'mail' with GID 12.
>>> Creating group 'man' with GID 15.
>>> Creating group 'mem' with GID 8.
>>> Creating group 'nobody' with GID 65534.
>>> Creating group 'render' with GID 105.
>>> Creating group 'root' with GID 0.
>>> Creating group 'sgx' with GID 106.
>>> Creating group 'sys' with GID 3.
>>> Creating group 'tape' with GID 33.
>>> Creating group 'tty' with GID 5.
>>> Creating group 'users' with GID 100.
>>> Creating group 'utmp' with GID 22.
>>> Creating group 'video' with GID 39.
>>> Creating group 'wheel' with GID 10.
>>> Creating user 'adm' (adm) with UID 3 and GID 4.
>>> Creating group 'bin' with GID 1.
>>> Creating user 'bin' (bin) with UID 1 and GID 1.
>>> Creating group 'daemon' with GID 2.
>>> Creating user 'daemon' (daemon) with UID 2 and GID 2.
>>> Creating user 'ftp' (FTP User) with UID 14 and GID 50.
>>> Creating user 'games' (games) with UID 12 and GID 100.
>>> Creating user 'halt' (halt) with UID 7 and GID 0.
>>> Creating user 'lp' (lp) with UID 4 and GID 7.
>>> Creating user 'mail' (mail) with UID 8 and GID 12.
>>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534.
>>> Creating user 'operator' (operator) with UID 11 and GID 0.
>>> Creating user 'root' (Super User) with UID 0 and GID 0.
>>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0.
>>> Creating user 'sync' (sync) with UID 5 and GID 0.
>>> 
[ 12/184] Installing setup-0:2.15.0-28. 100% |  54.9 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/184] Installing filesystem-0:3.18- 100% |   2.9 MiB/s | 212.8 KiB |  00m00s
[ 14/184] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[ 15/184] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB |  00m00s
[ 16/184] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB |  00m00s
[ 17/184] Installing coreutils-common-0 100% | 415.9 MiB/s |  11.2 MiB |  00m00s
[ 18/184] Installing ncurses-base-0:6.5 100% |  86.3 MiB/s | 353.5 KiB |  00m00s
[ 19/184] Installing bash-0:5.3.9-3.fc4 100% | 292.5 MiB/s |   8.5 MiB |  00m00s
[ 20/184] Installing glibc-common-0:2.4 100% |  68.3 MiB/s |   1.0 MiB |  00m00s
[ 21/184] Installing glibc-gconv-extra- 100% | 324.6 MiB/s |   7.5 MiB |  00m00s
[ 22/184] Installing glibc-0:2.42.9000- 100% | 193.1 MiB/s |   7.0 MiB |  00m00s
[ 23/184] Installing ncurses-libs-0:6.5 100% | 316.2 MiB/s | 971.5 KiB |  00m00s
[ 24/184] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 25/184] Installing zlib-ng-compat-0:2 100% | 166.4 MiB/s | 170.4 KiB |  00m00s
[ 26/184] Installing bzip2-libs-0:1.0.8 100% |   0.0   B/s |  81.6 KiB |  00m00s
[ 27/184] Installing libgpg-error-0:1.5 100% |  66.1 MiB/s | 947.5 KiB |  00m00s
[ 28/184] Installing libstdc++-0:16.0.1 100% | 416.9 MiB/s |   2.9 MiB |  00m00s
[ 29/184] Installing libassuan-0:2.5.7- 100% | 161.8 MiB/s | 165.7 KiB |  00m00s
[ 30/184] Installing libgcrypt-0:1.11.2 100% | 394.0 MiB/s |   1.6 MiB |  00m00s
[ 31/184] Installing readline-0:8.3-4.f 100% | 254.7 MiB/s | 521.6 KiB |  00m00s
[ 32/184] Installing gmp-1:6.3.0-5.fc44 100% | 399.2 MiB/s | 817.5 KiB |  00m00s
[ 33/184] Installing xz-libs-1:5.8.2-2. 100% | 213.7 MiB/s | 218.8 KiB |  00m00s
[ 34/184] Installing libuuid-0:2.41.3-1 100% |   0.0   B/s |  38.2 KiB |  00m00s
[ 35/184] Installing popt-0:1.19-10.fc4 100% |  68.0 MiB/s | 139.3 KiB |  00m00s
[ 36/184] Installing libzstd-0:1.5.7-5. 100% | 311.6 MiB/s | 957.4 KiB |  00m00s
[ 37/184] Installing elfutils-libelf-0: 100% | 376.3 MiB/s |   1.1 MiB |  00m00s
[ 38/184] Installing npth-0:1.8-4.fc44. 100% |   0.0   B/s |  50.6 KiB |  00m00s
[ 39/184] Installing libblkid-0:2.41.3- 100% | 269.0 MiB/s | 275.4 KiB |  00m00s
[ 40/184] Installing systemd-libs-0:259 100% | 348.9 MiB/s |   2.4 MiB |  00m00s
[ 41/184] Installing libxcrypt-0:4.5.2- 100% | 289.0 MiB/s | 295.9 KiB |  00m00s
[ 42/184] Installing libsepol-0:3.9-3.f 100% | 421.3 MiB/s | 862.8 KiB |  00m00s
[ 43/184] Installing sqlite-libs-0:3.51 100% | 397.6 MiB/s |   1.6 MiB |  00m00s
[ 44/184] Installing gnupg2-gpgconf-0:2 100% |  18.9 MiB/s | 251.8 KiB |  00m00s
[ 45/184] Installing libattr-0:2.5.2-8. 100% |   0.0   B/s |  25.2 KiB |  00m00s
[ 46/184] Installing libacl-0:2.3.2-6.f 100% |   0.0   B/s |  36.6 KiB |  00m00s
[ 47/184] Installing pcre2-0:10.47-1.fc 100% | 351.6 MiB/s | 720.0 KiB |  00m00s
[ 48/184] Installing libselinux-0:3.9-7 100% | 197.5 MiB/s | 202.3 KiB |  00m00s
[ 49/184] Installing grep-0:3.12-3.fc44 100% |  62.7 MiB/s |   1.0 MiB |  00m00s
[ 50/184] Installing sed-0:4.9-7.fc44.x 100% |  56.3 MiB/s | 865.4 KiB |  00m00s
[ 51/184] Installing findutils-1:4.10.0 100% | 110.0 MiB/s |   1.9 MiB |  00m00s
[ 52/184] Installing libtasn1-0:4.20.0- 100% | 177.7 MiB/s | 182.0 KiB |  00m00s
[ 53/184] Installing libunistring-0:1.1 100% | 346.9 MiB/s |   1.7 MiB |  00m00s
[ 54/184] Installing libidn2-0:2.3.8-3. 100% |  68.7 MiB/s | 562.6 KiB |  00m00s
[ 55/184] Installing crypto-policies-0: 100% |  38.5 MiB/s | 157.7 KiB |  00m00s
[ 56/184] Installing xz-1:5.8.2-2.fc44. 100% |  76.1 MiB/s |   1.4 MiB |  00m00s
[ 57/184] Installing libmount-0:2.41.3- 100% | 190.3 MiB/s | 389.7 KiB |  00m00s
[ 58/184] Installing gnupg2-verify-0:2. 100% |  27.2 MiB/s | 361.7 KiB |  00m00s
[ 59/184] Installing dwz-0:0.16-3.fc44. 100% |  23.8 MiB/s | 292.3 KiB |  00m00s
[ 60/184] Installing mpfr-0:4.2.2-3.fc4 100% | 276.9 MiB/s | 850.8 KiB |  00m00s
[ 61/184] Installing gawk-0:5.3.2-3.fc4 100% | 107.9 MiB/s |   1.8 MiB |  00m00s
[ 62/184] Installing libksba-0:1.6.7-5. 100% | 203.6 MiB/s | 416.9 KiB |  00m00s
[ 63/184] Installing unzip-0:6.0-69.fc4 100% |  33.8 MiB/s | 449.3 KiB |  00m00s
[ 64/184] Installing file-libs-0:5.46-9 100% | 659.0 MiB/s |  11.9 MiB |  00m00s
[ 65/184] Installing file-0:5.46-9.fc44 100% |   8.3 MiB/s | 101.6 KiB |  00m00s
[ 66/184] Installing diffutils-0:3.12-5 100% |  98.3 MiB/s |   1.6 MiB |  00m00s
[ 67/184] Installing libeconf-0:0.7.9-3 100% |  64.9 MiB/s |  66.4 KiB |  00m00s
[ 68/184] Installing libcap-ng-0:0.9-5. 100% |  68.9 MiB/s |  70.5 KiB |  00m00s
[ 69/184] Installing audit-libs-0:4.1.2 100% | 191.9 MiB/s | 392.9 KiB |  00m00s
[ 70/184] Installing pam-libs-0:1.7.2-1 100% | 129.8 MiB/s | 132.9 KiB |  00m00s
[ 71/184] Installing libcap-0:2.77-2.fc 100% |  16.3 MiB/s | 217.2 KiB |  00m00s
[ 72/184] Installing libsemanage-0:3.9- 100% | 306.7 MiB/s | 314.1 KiB |  00m00s
[ 73/184] Installing libsmartcols-0:2.4 100% | 184.9 MiB/s | 189.3 KiB |  00m00s
[ 74/184] Installing lua-libs-0:5.4.8-5 100% | 276.6 MiB/s | 283.2 KiB |  00m00s
[ 75/184] Installing json-c-0:0.18-8.fc 100% |  81.9 MiB/s |  83.9 KiB |  00m00s
[ 76/184] Installing libffi-0:3.5.2-2.f 100% |  87.0 MiB/s |  89.1 KiB |  00m00s
[ 77/184] Installing p11-kit-0:0.25.8-2 100% | 121.9 MiB/s |   2.3 MiB |  00m00s
[ 78/184] Installing alternatives-0:1.3 100% |   5.2 MiB/s |  63.6 KiB |  00m00s
[ 79/184] Installing p11-kit-trust-0:0. 100% |  23.6 MiB/s | 460.0 KiB |  00m00s
[ 80/184] Installing ngtcp2-0:1.19.0-2. 100% | 162.0 MiB/s | 331.7 KiB |  00m00s
[ 81/184] Installing openssl-libs-1:3.5 100% | 399.3 MiB/s |   9.2 MiB |  00m00s
[ 82/184] Installing coreutils-0:9.9-4. 100% | 161.3 MiB/s |   5.5 MiB |  00m00s
[ 83/184] Installing ca-certificates-0: 100% |   2.1 MiB/s |   2.5 MiB |  00m01s
[ 84/184] Installing gzip-0:1.14-2.fc44 100% |  28.4 MiB/s | 407.1 KiB |  00m00s
[ 85/184] Installing rpm-sequoia-0:1.10 100% | 411.0 MiB/s |   2.5 MiB |  00m00s
[ 86/184] Installing libfsverity-0:1.6- 100% |   0.0   B/s |  29.4 KiB |  00m00s
[ 87/184] Installing libevent-0:2.1.12- 100% | 319.8 MiB/s | 982.4 KiB |  00m00s
[ 88/184] Installing ngtcp2-crypto-ossl 100% |  51.2 MiB/s |  52.5 KiB |  00m00s
[ 89/184] Installing util-linux-core-0: 100% |  87.2 MiB/s |   1.5 MiB |  00m00s
[ 90/184] Installing zip-0:3.0-45.fc44. 100% |  52.7 MiB/s | 701.9 KiB |  00m00s
[ 91/184] Installing gnupg2-keyboxd-0:2 100% |  33.0 MiB/s | 202.5 KiB |  00m00s
[ 92/184] Installing libpsl-0:0.21.5-7. 100% |  75.6 MiB/s |  77.4 KiB |  00m00s
[ 93/184] Installing tar-2:1.35-8.fc44. 100% | 148.9 MiB/s |   3.0 MiB |  00m00s
[ 94/184] Installing linkdupes-0:0.7.2- 100% |  57.8 MiB/s | 828.0 KiB |  00m00s
[ 95/184] Installing libselinux-utils-0 100% |  24.0 MiB/s | 319.9 KiB |  00m00s
[ 96/184] Installing liblastlog2-0:2.41 100% |   6.5 MiB/s |  39.8 KiB |  00m00s
[ 97/184] Installing systemd-standalone 100% |  22.7 MiB/s | 302.1 KiB |  00m00s
[ 98/184] Installing rpm-libs-0:6.0.1-2 100% | 313.4 MiB/s | 962.8 KiB |  00m00s
[ 99/184] Installing libusb1-0:1.0.29-5 100% |  24.7 MiB/s | 176.9 KiB |  00m00s
>>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.x86_64
>>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.x86_64
>>> Scriptlet output:
>>> Creating group 'tss' with GID 59.
>>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59.
>>> 
[100/184] Installing tpm2-tss-0:4.1.3-9 100% | 272.2 MiB/s |   1.6 MiB |  00m00s
[101/184] Installing ima-evm-utils-libs 100% |  60.4 MiB/s |  61.9 KiB |  00m00s
[102/184] Installing gnupg2-gpg-agent-0 100% |  31.9 MiB/s | 686.5 KiB |  00m00s
[103/184] Installing libfdisk-0:2.41.3- 100% | 126.8 MiB/s | 389.4 KiB |  00m00s
[104/184] Installing util-linux-0:2.41. 100% | 105.4 MiB/s |   3.6 MiB |  00m00s
[105/184] Installing policycoreutils-0: 100% |  37.1 MiB/s | 912.3 KiB |  00m00s
[106/184] Installing selinux-policy-0:4 100% |   1.7 MiB/s |  33.6 KiB |  00m00s
[107/184] Installing selinux-policy-tar 100% | 197.3 MiB/s |  14.8 MiB |  00m00s
[108/184] Installing zstd-0:1.5.7-5.fc4 100% |  30.9 MiB/s | 506.0 KiB |  00m00s
[109/184] Installing libxml2-0:2.12.10- 100% | 110.7 MiB/s |   1.8 MiB |  00m00s
[110/184] Installing nettle-0:3.10.1-3. 100% | 259.6 MiB/s | 797.4 KiB |  00m00s
[111/184] Installing gnutls-0:3.8.11-10 100% | 373.1 MiB/s |   3.7 MiB |  00m00s
[112/184] Installing bzip2-0:1.0.8-23.f 100% |   8.1 MiB/s |  99.5 KiB |  00m00s
[113/184] Installing add-determinism-0: 100% | 133.5 MiB/s |   2.3 MiB |  00m00s
[114/184] Installing build-reproducibil 100% |   0.0   B/s |   1.5 KiB |  00m00s
[115/184] Installing cpio-0:2.15-6.fc43 100% |  78.5 MiB/s |   1.1 MiB |  00m00s
[116/184] Installing ed-0:1.22.4-2.fc44 100% |  13.4 MiB/s | 151.4 KiB |  00m00s
[117/184] Installing patch-0:2.8-4.fc44 100% |  18.6 MiB/s | 228.1 KiB |  00m00s
[118/184] Installing lz4-libs-0:1.10.0- 100% | 154.6 MiB/s | 158.4 KiB |  00m00s
[119/184] Installing libarchive-0:3.8.4 100% | 323.3 MiB/s | 993.1 KiB |  00m00s
[120/184] Installing libgomp-0:16.0.1-0 100% | 279.7 MiB/s | 572.9 KiB |  00m00s
[121/184] Installing libtool-ltdl-0:2.5 100% |   0.0   B/s |  71.1 KiB |  00m00s
[122/184] Installing gdbm-libs-1:1.23-1 100% | 128.3 MiB/s | 131.3 KiB |  00m00s
[123/184] Installing cyrus-sasl-lib-0:2 100% | 135.9 MiB/s |   2.3 MiB |  00m00s
[124/184] Installing openldap-0:2.6.10- 100% | 218.5 MiB/s | 671.3 KiB |  00m00s
[125/184] Installing gnupg2-dirmngr-0:2 100% |  32.7 MiB/s | 636.7 KiB |  00m00s
[126/184] Installing gnupg2-0:2.4.9-4.f 100% | 224.4 MiB/s |   6.5 MiB |  00m00s
[127/184] Installing rpm-sign-libs-0:6. 100% |  39.5 MiB/s |  40.5 KiB |  00m00s
[128/184] Installing gpgverify-0:2.2-4. 100% |   0.0   B/s |   9.4 KiB |  00m00s
[129/184] Installing jansson-0:2.14-4.f 100% |  88.2 MiB/s |  90.3 KiB |  00m00s
[130/184] Installing libpkgconf-0:2.3.0 100% |  77.3 MiB/s |  79.2 KiB |  00m00s
[131/184] Installing pkgconf-0:2.3.0-4. 100% |   7.4 MiB/s |  90.8 KiB |  00m00s
[132/184] Installing pkgconf-pkg-config 100% | 161.2 KiB/s |   1.8 KiB |  00m00s
[133/184] Installing xxhash-libs-0:0.8. 100% |  93.2 MiB/s |  95.4 KiB |  00m00s
[134/184] Installing libbrotli-0:1.2.0- 100% | 282.3 MiB/s | 867.3 KiB |  00m00s
[135/184] Installing libnghttp2-0:1.68. 100% | 163.3 MiB/s | 167.3 KiB |  00m00s
[136/184] Installing libnghttp3-0:1.15. 100% | 156.8 MiB/s | 160.6 KiB |  00m00s
[137/184] Installing keyutils-libs-0:1. 100% |  54.3 MiB/s |  55.6 KiB |  00m00s
[138/184] Installing libcom_err-0:1.47. 100% |  62.6 MiB/s |  64.1 KiB |  00m00s
[139/184] Installing libverto-0:0.3.2-1 100% |  26.4 MiB/s |  27.1 KiB |  00m00s
[140/184] Installing krb5-libs-0:1.21.3 100% | 337.9 MiB/s |   2.4 MiB |  00m00s
[141/184] Installing libssh-0:0.11.3-1. 100% | 277.9 MiB/s | 569.2 KiB |  00m00s
[142/184] Installing libcurl-0:8.18.0-3 100% | 331.4 MiB/s |   1.0 MiB |  00m00s
[143/184] Installing curl-0:8.18.0-3.fc 100% |  22.4 MiB/s | 482.6 KiB |  00m00s
[144/184] Installing rpm-0:6.0.1-2.fc44 100% |  85.0 MiB/s |   2.6 MiB |  00m00s
[145/184] Installing cmake-srpm-macros- 100% |   0.0   B/s | 804.0   B |  00m00s
[146/184] Installing efi-srpm-macros-0: 100% |   0.0   B/s |  41.2 KiB |  00m00s
[147/184] Installing java-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[148/184] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[149/184] Installing tree-sitter-srpm-m 100% |   0.0   B/s |   9.3 KiB |  00m00s
[150/184] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[151/184] Installing filesystem-srpm-ma 100% |   0.0   B/s |  38.9 KiB |  00m00s
[152/184] Installing elfutils-default-y 100% | 510.7 KiB/s |   2.0 KiB |  00m00s
[153/184] Installing elfutils-libs-0:0. 100% | 233.4 MiB/s | 717.0 KiB |  00m00s
[154/184] Installing elfutils-debuginfo 100% |   6.0 MiB/s |  86.0 KiB |  00m00s
[155/184] Installing elfutils-0:0.194-3 100% | 155.7 MiB/s |   3.0 MiB |  00m00s
[156/184] Installing binutils-0:2.45.50 100% | 327.2 MiB/s |  27.5 MiB |  00m00s
[157/184] Installing gdb-minimal-0:17.1 100% | 292.5 MiB/s |  14.3 MiB |  00m00s
[158/184] Installing debugedit-0:5.2-6. 100% |  15.5 MiB/s | 221.6 KiB |  00m00s
[159/184] Installing rpm-build-libs-0:6 100% | 270.6 MiB/s | 277.1 KiB |  00m00s
[160/184] Installing rust-srpm-macros-0 100% |   0.0   B/s |   6.4 KiB |  00m00s
[161/184] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 740.0   B |  00m00s
[162/184] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[163/184] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[164/184] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[165/184] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[166/184] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.1 KiB |  00m00s
[167/184] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[168/184] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[169/184] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[170/184] Installing gap-srpm-macros-0: 100% |   0.0   B/s |   2.7 KiB |  00m00s
[171/184] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[172/184] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[173/184] Installing redhat-rpm-config- 100% |  92.7 MiB/s | 189.9 KiB |  00m00s
[174/184] Installing forge-srpm-macros- 100% |   0.0   B/s |  40.3 KiB |  00m00s
[175/184] Installing fonts-srpm-macros- 100% |  11.1 MiB/s |  57.0 KiB |  00m00s
[176/184] Installing go-srpm-macros-0:3 100% |  61.6 MiB/s |  63.0 KiB |  00m00s
[177/184] Installing rpm-build-0:6.0.1- 100% |  21.2 MiB/s | 303.7 KiB |  00m00s
[178/184] Installing pyproject-srpm-mac 100% |   0.0   B/s |   2.5 KiB |  00m00s
[179/184] Installing R-srpm-macros-0:1. 100% |   0.0   B/s |   4.2 KiB |  00m00s
[180/184] Installing python-srpm-macros 100% |   0.0   B/s |  52.9 KiB |  00m00s
[181/184] Installing rpm-plugin-selinux 100% |   0.0   B/s |  12.9 KiB |  00m00s
[182/184] Installing which-0:2.23-4.fc4 100% |   6.4 MiB/s |  85.6 KiB |  00m00s
[183/184] Installing shadow-utils-2:4.1 100% | 147.1 MiB/s |   4.0 MiB |  00m00s
[184/184] Installing info-0:7.2-7.fc44. 100% |  49.7 KiB/s | 358.3 KiB |  00m07s
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: R-srpm-macros-1.3.4-3.fc44.noarch
add-determinism-0.7.2-3.fc44.x86_64
alternatives-1.33-5.fc44.x86_64
ansible-srpm-macros-1-20.1.fc44.noarch
audit-libs-4.1.2-4.fc44.x86_64
bash-5.3.9-3.fc44.x86_64
binutils-2.45.50-19.fc44.x86_64
build-reproducibility-srpm-macros-0.7.2-3.fc44.noarch
bzip2-1.0.8-23.fc44.x86_64
bzip2-libs-1.0.8-23.fc44.x86_64
ca-certificates-2025.2.80_v9.0.304-5.fc44.noarch
cmake-srpm-macros-3.31.10-5.fc44.noarch
coreutils-9.9-4.fc44.x86_64
coreutils-common-9.9-4.fc44.x86_64
cpio-2.15-6.fc43.x86_64
crypto-policies-20251128-3.git19878fe.fc44.noarch
curl-8.18.0-3.fc44.x86_64
cyrus-sasl-lib-2.1.28-35.fc44.x86_64
debugedit-5.2-6.fc44.x86_64
diffutils-3.12-5.fc44.x86_64
dwz-0.16-3.fc44.x86_64
ed-1.22.4-2.fc44.x86_64
efi-srpm-macros-6-6.fc44.noarch
elfutils-0.194-3.fc44.x86_64
elfutils-debuginfod-client-0.194-3.fc44.x86_64
elfutils-default-yama-scope-0.194-3.fc44.noarch
elfutils-libelf-0.194-3.fc44.x86_64
elfutils-libs-0.194-3.fc44.x86_64
fedora-gpg-keys-44-0.1.noarch
fedora-release-44-0.10.noarch
fedora-release-common-44-0.10.noarch
fedora-release-identity-basic-44-0.10.noarch
fedora-repos-44-0.1.noarch
fedora-repos-rawhide-44-0.1.noarch
file-5.46-9.fc44.x86_64
file-libs-5.46-9.fc44.x86_64
filesystem-3.18-52.fc44.x86_64
filesystem-srpm-macros-3.18-52.fc44.noarch
findutils-4.10.0-7.fc44.x86_64
fonts-srpm-macros-5.0.0-2.fc44.noarch
forge-srpm-macros-0.4.0-4.fc44.noarch
fpc-srpm-macros-1.3-16.fc44.noarch
gap-srpm-macros-2-2.fc44.noarch
gawk-5.3.2-3.fc44.x86_64
gdb-minimal-17.1-2.fc44.x86_64
gdbm-libs-1.23-11.fc44.x86_64
ghc-srpm-macros-1.9.2-4.fc44.noarch
glibc-2.42.9000-25.fc44.x86_64
glibc-common-2.42.9000-25.fc44.x86_64
glibc-gconv-extra-2.42.9000-25.fc44.x86_64
glibc-minimal-langpack-2.42.9000-25.fc44.x86_64
gmp-6.3.0-5.fc44.x86_64
gnat-srpm-macros-7-2.fc44.noarch
gnulib-l10n-20241231-2.fc44.noarch
gnupg2-2.4.9-4.fc44.x86_64
gnupg2-dirmngr-2.4.9-4.fc44.x86_64
gnupg2-gpg-agent-2.4.9-4.fc44.x86_64
gnupg2-gpgconf-2.4.9-4.fc44.x86_64
gnupg2-keyboxd-2.4.9-4.fc44.x86_64
gnupg2-verify-2.4.9-4.fc44.x86_64
gnutls-3.8.11-10.fc44.x86_64
go-srpm-macros-3.8.0-2.fc44.noarch
gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b
gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98
gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf
gpgverify-2.2-4.fc44.noarch
grep-3.12-3.fc44.x86_64
gzip-1.14-2.fc44.x86_64
ima-evm-utils-libs-1.6.2-8.fc44.x86_64
info-7.2-7.fc44.x86_64
jansson-2.14-4.fc44.x86_64
java-srpm-macros-1-8.fc44.noarch
json-c-0.18-8.fc44.x86_64
kernel-srpm-macros-1.0-28.fc44.noarch
keyutils-libs-1.6.3-7.fc44.x86_64
krb5-libs-1.21.3-12.fc44.x86_64
libacl-2.3.2-6.fc44.x86_64
libarchive-3.8.4-2.fc44.x86_64
libassuan-2.5.7-5.fc44.x86_64
libattr-2.5.2-8.fc44.x86_64
libblkid-2.41.3-12.fc44.x86_64
libbrotli-1.2.0-3.fc44.x86_64
libcap-2.77-2.fc44.x86_64
libcap-ng-0.9-5.fc44.x86_64
libcom_err-1.47.3-4.fc44.x86_64
libcurl-8.18.0-3.fc44.x86_64
libeconf-0.7.9-3.fc44.x86_64
libevent-2.1.12-17.fc44.x86_64
libfdisk-2.41.3-12.fc44.x86_64
libffi-3.5.2-2.fc44.x86_64
libfsverity-1.6-4.fc44.x86_64
libgcc-16.0.1-0.3.fc44.1.x86_64
libgcrypt-1.11.2-1.fc44.x86_64
libgomp-16.0.1-0.3.fc44.1.x86_64
libgpg-error-1.58-2.fc44.x86_64
libidn2-2.3.8-3.fc44.x86_64
libksba-1.6.7-5.fc44.x86_64
liblastlog2-2.41.3-12.fc44.x86_64
libmount-2.41.3-12.fc44.x86_64
libnghttp2-1.68.0-3.fc44.x86_64
libnghttp3-1.15.0-1.fc44.x86_64
libpkgconf-2.3.0-4.fc44.x86_64
libpsl-0.21.5-7.fc44.x86_64
libselinux-3.9-7.fc44.x86_64
libselinux-utils-3.9-7.fc44.x86_64
libsemanage-3.9-5.fc44.x86_64
libsepol-3.9-3.fc44.x86_64
libsmartcols-2.41.3-12.fc44.x86_64
libssh-0.11.3-1.fc44.x86_64
libssh-config-0.11.3-1.fc44.noarch
libstdc++-16.0.1-0.3.fc44.1.x86_64
libtasn1-4.20.0-3.fc44.x86_64
libtool-ltdl-2.5.4-10.fc44.x86_64
libunistring-1.1-11.fc44.x86_64
libusb1-1.0.29-5.fc44.x86_64
libuuid-2.41.3-12.fc44.x86_64
libverto-0.3.2-12.fc44.x86_64
libxcrypt-4.5.2-3.fc44.x86_64
libxml2-2.12.10-6.fc44.x86_64
libzstd-1.5.7-5.fc44.x86_64
linkdupes-0.7.2-3.fc44.x86_64
lua-libs-5.4.8-5.fc44.x86_64
lua-srpm-macros-1-17.fc44.noarch
lz4-libs-1.10.0-4.fc44.x86_64
mpfr-4.2.2-3.fc44.x86_64
ncurses-base-6.5-9.20250614.fc44.noarch
ncurses-libs-6.5-9.20250614.fc44.x86_64
nettle-3.10.1-3.fc44.x86_64
ngtcp2-1.19.0-2.fc44.x86_64
ngtcp2-crypto-ossl-1.19.0-2.fc44.x86_64
npth-1.8-4.fc44.x86_64
ocaml-srpm-macros-11-3.fc44.noarch
openblas-srpm-macros-2-21.fc44.noarch
openldap-2.6.10-7.fc44.x86_64
openssl-libs-3.5.4-2.fc44.x86_64
p11-kit-0.25.8-2.fc44.x86_64
p11-kit-trust-0.25.8-2.fc44.x86_64
package-notes-srpm-macros-0.5-15.fc44.noarch
pam-libs-1.7.2-1.fc44.x86_64
patch-2.8-4.fc44.x86_64
pcre2-10.47-1.fc44.1.x86_64
pcre2-syntax-10.47-1.fc44.1.noarch
perl-srpm-macros-1-61.fc44.noarch
pkgconf-2.3.0-4.fc44.x86_64
pkgconf-m4-2.3.0-4.fc44.noarch
pkgconf-pkg-config-2.3.0-4.fc44.x86_64
policycoreutils-3.9-8.fc44.x86_64
popt-1.19-10.fc44.x86_64
publicsuffix-list-dafsa-20260116-1.fc44.noarch
pyproject-srpm-macros-1.18.6-2.fc44.noarch
python-srpm-macros-3.14-10.fc44.noarch
qt5-srpm-macros-5.15.18-2.fc44.noarch
qt6-srpm-macros-6.10.1-2.fc44.noarch
readline-8.3-4.fc44.x86_64
redhat-rpm-config-343-19.fc44.noarch
rpm-6.0.1-2.fc44.x86_64
rpm-build-6.0.1-2.fc44.x86_64
rpm-build-libs-6.0.1-2.fc44.x86_64
rpm-libs-6.0.1-2.fc44.x86_64
rpm-plugin-selinux-6.0.1-2.fc44.x86_64
rpm-sequoia-1.10.0-2.fc44.x86_64
rpm-sign-libs-6.0.1-2.fc44.x86_64
rust-srpm-macros-28.4-3.fc44.noarch
sed-4.9-7.fc44.x86_64
selinux-policy-42.22-1.fc44.noarch
selinux-policy-targeted-42.22-1.fc44.noarch
setup-2.15.0-28.fc44.noarch
shadow-utils-4.18.0-7.fc44.x86_64
sqlite-libs-3.51.2-1.fc44.x86_64
systemd-libs-259-9.fc44.x86_64
systemd-standalone-sysusers-259-9.fc44.x86_64
tar-1.35-8.fc44.x86_64
tpm2-tss-4.1.3-9.fc44.x86_64
tree-sitter-srpm-macros-0.4.2-2.fc44.noarch
unzip-6.0-69.fc44.x86_64
util-linux-2.41.3-12.fc44.x86_64
util-linux-core-2.41.3-12.fc44.x86_64
which-2.23-4.fc44.x86_64
xxhash-libs-0.8.3-4.fc44.x86_64
xz-5.8.2-2.fc44.x86_64
xz-libs-5.8.2-2.fc44.x86_64
zig-srpm-macros-1-8.fc44.noarch
zip-3.0-45.fc44.x86_64
zlib-ng-compat-2.3.2-3.fc44.x86_64
zstd-1.5.7-5.fc44.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.fc44.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1769501806.001017/root/var/log/dnf5.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-d1503i_u/samtools/samtools.spec) Config(child) 0 minutes 30 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/samtools-1.23-1.fc44.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1769501806.001017/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1769501806.001017/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/fedora-rawhide-x86_64-1769501806.001017/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-6.0.1-2.fc44.x86_64
  rpm-sequoia-1.10.0-2.fc44.x86_64
  dnf5-5.3.0.0-7.fc44.x86_64
  dnf5-plugins-5.3.0.0-7.fc44.x86_64
Finish: chroot init
Start: build phase for samtools-1.23-1.fc44.src.rpm
Start: build setup for samtools-1.23-1.fc44.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |   2.8 KiB/s |   1.5 KiB |  00m01s
 fedora                                 100% |  43.4 KiB/s |  26.4 KiB |  00m01s
Repositories loaded.
Package                 Arch   Version                Repository      Size
Installing:
 gcc                    x86_64 0:16.0.1-0.3.fc44.1    fedora     120.6 MiB
 htslib-devel           x86_64 0:1.23-1.fc44          copr_base  449.9 KiB
 htslib-tools           x86_64 0:1.23-1.fc44          copr_base    4.0 MiB
 make                   x86_64 1:4.4.1-12.fc44        fedora       1.8 MiB
 ncurses-devel          x86_64 0:6.5-9.20250614.fc44  fedora     893.4 KiB
 perl-FindBin           noarch 0:1.54-521.fc44        fedora       6.8 KiB
 perl-Getopt-Long       noarch 1:2.58-521.fc44        fedora     144.5 KiB
 perl-interpreter       x86_64 4:5.42.0-521.fc44      fedora     118.5 KiB
 perl-lib               x86_64 0:0.65-521.fc44        fedora       8.5 KiB
 zlib-ng-compat-devel   x86_64 0:2.3.2-3.fc44         fedora     107.0 KiB
Installing dependencies:
 annobin-docs           noarch 0:13.05-3.fc44         fedora      99.2 KiB
 annobin-plugin-gcc     x86_64 0:13.05-3.fc44         fedora     695.7 KiB
 cmake-filesystem       x86_64 0:3.31.10-5.fc44       fedora       0.0   B
 cpp                    x86_64 0:16.0.1-0.3.fc44.1    fedora      42.1 MiB
 gcc-plugin-annobin     x86_64 0:16.0.1-0.3.fc44.1    fedora      57.2 KiB
 glibc-devel            x86_64 0:2.42.9000-25.fc44    fedora       2.3 MiB
 groff-base             x86_64 0:1.23.0-12.fc44       fedora       3.9 MiB
 htslib                 x86_64 0:1.23-1.fc44          copr_base    1.4 MiB
 kernel-headers         x86_64 0:6.19.0-0.rc6.43.fc44 fedora       6.9 MiB
 libatomic              x86_64 0:16.0.1-0.3.fc44.1    fedora      45.3 KiB
 libmpc                 x86_64 0:1.3.1-9.fc44         fedora     160.4 KiB
 libxcrypt-devel        x86_64 0:4.5.2-3.fc44         fedora      31.0 KiB
 ncurses                x86_64 0:6.5-9.20250614.fc44  fedora     608.7 KiB
 ncurses-c++-libs       x86_64 0:6.5-9.20250614.fc44  fedora     161.5 KiB
 perl-AutoLoader        noarch 0:5.74-521.fc44        fedora      20.6 KiB
 perl-B                 x86_64 0:1.89-521.fc44        fedora     501.2 KiB
 perl-Carp              noarch 0:1.54-521.fc44        fedora      46.6 KiB
 perl-Class-Struct      noarch 0:0.68-521.fc44        fedora      25.4 KiB
 perl-Data-Dumper       x86_64 0:2.191-522.fc44       fedora     115.5 KiB
 perl-Digest            noarch 0:1.20-521.fc44        fedora      35.3 KiB
 perl-Digest-MD5        x86_64 0:2.59-521.fc44        fedora      59.6 KiB
 perl-DynaLoader        x86_64 0:1.57-521.fc44        fedora      32.1 KiB
 perl-Encode            x86_64 4:3.21-521.fc44        fedora       4.7 MiB
 perl-Errno             x86_64 0:1.38-521.fc44        fedora       8.4 KiB
 perl-Exporter          noarch 0:5.79-521.fc44        fedora      54.3 KiB
 perl-Fcntl             x86_64 0:1.20-521.fc44        fedora      48.7 KiB
 perl-File-Basename     noarch 0:2.86-521.fc44        fedora      14.0 KiB
 perl-File-Path         noarch 0:2.18-522.fc44        fedora      63.5 KiB
 perl-File-Temp         noarch 1:0.231.200-2.fc44     fedora     163.7 KiB
 perl-File-stat         noarch 0:1.14-521.fc44        fedora      12.5 KiB
 perl-FileHandle        noarch 0:2.05-521.fc44        fedora       9.4 KiB
 perl-Getopt-Std        noarch 0:1.14-521.fc44        fedora      11.2 KiB
 perl-HTTP-Tiny         noarch 0:0.092-2.fc44         fedora     157.6 KiB
 perl-IO                x86_64 0:1.55-521.fc44        fedora     147.3 KiB
 perl-IO-Socket-IP      noarch 0:0.43-522.fc44        fedora     100.3 KiB
 perl-IO-Socket-SSL     noarch 0:2.098-2.fc44         fedora     723.5 KiB
 perl-IPC-Open3         noarch 0:1.24-521.fc44        fedora      27.7 KiB
 perl-MIME-Base32       noarch 0:1.303-25.fc44        fedora      30.7 KiB
 perl-MIME-Base64       x86_64 0:3.16-521.fc44        fedora      41.9 KiB
 perl-Net-SSLeay        x86_64 0:1.94-12.fc44         fedora       1.3 MiB
 perl-POSIX             x86_64 0:2.23-521.fc44        fedora     231.2 KiB
 perl-PathTools         x86_64 0:3.94-521.fc44        fedora     179.9 KiB
 perl-Pod-Escapes       noarch 1:1.07-521.fc44        fedora      24.9 KiB
 perl-Pod-Perldoc       noarch 0:3.28.01-522.fc44     fedora     163.7 KiB
 perl-Pod-Simple        noarch 1:3.47-4.fc44          fedora     565.3 KiB
 perl-Pod-Usage         noarch 4:2.05-521.fc44        fedora      86.3 KiB
 perl-Scalar-List-Utils x86_64 5:1.70-2.fc44          fedora     144.8 KiB
 perl-SelectSaver       noarch 0:1.02-521.fc44        fedora       2.2 KiB
 perl-Socket            x86_64 4:2.040-3.fc44         fedora     120.1 KiB
 perl-Storable          x86_64 1:3.37-522.fc44        fedora     235.1 KiB
 perl-Symbol            noarch 0:1.09-521.fc44        fedora       6.8 KiB
 perl-Term-ANSIColor    noarch 0:5.01-522.fc44        fedora      97.5 KiB
 perl-Term-Cap          noarch 0:1.18-521.fc44        fedora      29.3 KiB
 perl-Text-ParseWords   noarch 0:3.31-521.fc44        fedora      13.6 KiB
 perl-Text-Tabs+Wrap    noarch 0:2024.001-521.fc44    fedora      22.6 KiB
 perl-Time-HiRes        x86_64 4:1.9778-521.fc44      fedora     115.6 KiB
 perl-Time-Local        noarch 2:1.350-521.fc44       fedora      69.0 KiB
 perl-URI               noarch 0:5.34-3.fc44          fedora     268.0 KiB
 perl-base              noarch 0:2.27-521.fc44        fedora      12.6 KiB
 perl-constant          noarch 0:1.33-522.fc44        fedora      26.2 KiB
 perl-if                noarch 0:0.61.000-521.fc44    fedora       5.8 KiB
 perl-libnet            noarch 0:3.15-522.fc44        fedora     289.4 KiB
 perl-libs              x86_64 4:5.42.0-521.fc44      fedora      11.6 MiB
 perl-locale            noarch 0:1.13-521.fc44        fedora       6.1 KiB
 perl-mro               x86_64 0:1.29-521.fc44        fedora      41.5 KiB
 perl-overload          noarch 0:1.40-521.fc44        fedora      71.6 KiB
 perl-overloading       noarch 0:0.02-521.fc44        fedora       4.9 KiB
 perl-parent            noarch 1:0.244-521.fc44       fedora      10.3 KiB
 perl-podlators         noarch 1:6.0.2-521.fc44       fedora     317.5 KiB
 perl-vars              noarch 0:1.05-521.fc44        fedora       3.9 KiB

Transaction Summary:
 Installing:        80 packages

Total size of inbound packages is 72 MiB. Need to download 72 MiB.
After this operation, 209 MiB extra will be used (install 209 MiB, remove 0 B).
[ 1/80] perl-FindBin-0:1.54-521.fc44.no 100% | 152.6 KiB/s |  13.9 KiB |  00m00s
[ 2/80] perl-Getopt-Long-1:2.58-521.fc4 100% |   1.2 MiB/s |  63.6 KiB |  00m00s
[ 3/80] perl-lib-0:0.65-521.fc44.x86_64 100% | 634.2 KiB/s |  14.6 KiB |  00m00s
[ 4/80] make-1:4.4.1-12.fc44.x86_64     100% |   2.9 MiB/s | 588.7 KiB |  00m00s
[ 5/80] perl-interpreter-4:5.42.0-521.f 100% |   2.1 MiB/s |  72.0 KiB |  00m00s
[ 6/80] htslib-devel-0:1.23-1.fc44.x86_ 100% | 440.1 KiB/s | 106.9 KiB |  00m00s
[ 7/80] gcc-0:16.0.1-0.3.fc44.1.x86_64  100% |  85.6 MiB/s |  43.0 MiB |  00m01s
[ 8/80] ncurses-devel-0:6.5-9.20250614. 100% |   9.0 MiB/s | 590.1 KiB |  00m00s
[ 9/80] htslib-tools-0:1.23-1.fc44.x86_ 100% |   2.6 MiB/s | 801.1 KiB |  00m00s
[10/80] zlib-ng-compat-devel-0:2.3.2-3. 100% |   1.7 MiB/s |  38.0 KiB |  00m00s
[11/80] libmpc-0:1.3.1-9.fc44.x86_64    100% |   2.0 MiB/s |  72.1 KiB |  00m00s
[12/80] perl-Carp-0:1.54-521.fc44.noarc 100% |   1.4 MiB/s |  28.8 KiB |  00m00s
[13/80] perl-File-Basename-0:2.86-521.f 100% | 841.7 KiB/s |  16.8 KiB |  00m00s
[14/80] perl-Exporter-0:5.79-521.fc44.n 100% |   1.1 MiB/s |  30.8 KiB |  00m00s
[15/80] perl-PathTools-0:3.94-521.fc44. 100% |   4.3 MiB/s |  87.3 KiB |  00m00s
[16/80] cpp-0:16.0.1-0.3.fc44.1.x86_64  100% | 103.2 MiB/s |  14.4 MiB |  00m00s
[17/80] perl-Pod-Usage-4:2.05-521.fc44. 100% | 542.1 KiB/s |  40.7 KiB |  00m00s
[18/80] perl-Text-ParseWords-0:3.31-521 100% | 289.0 KiB/s |  16.5 KiB |  00m00s
[19/80] perl-base-0:2.27-521.fc44.noarc 100% | 793.9 KiB/s |  15.9 KiB |  00m00s
[20/80] perl-constant-0:1.33-522.fc44.n 100% |   1.1 MiB/s |  22.9 KiB |  00m00s
[21/80] perl-overload-0:1.40-521.fc44.n 100% |   1.7 MiB/s |  45.2 KiB |  00m00s
[22/80] perl-libs-4:5.42.0-521.fc44.x86 100% |  78.1 MiB/s |   2.6 MiB |  00m00s
[23/80] ncurses-c++-libs-0:6.5-9.202506 100% |   1.4 MiB/s |  39.9 KiB |  00m00s
[24/80] cmake-filesystem-0:3.31.10-5.fc 100% | 707.0 KiB/s |  14.1 KiB |  00m00s
[25/80] perl-Errno-0:1.38-521.fc44.x86_ 100% | 729.4 KiB/s |  14.6 KiB |  00m00s
[26/80] perl-Scalar-List-Utils-5:1.70-2 100% |   3.7 MiB/s |  75.4 KiB |  00m00s
[27/80] perl-Pod-Perldoc-0:3.28.01-522. 100% |   4.0 MiB/s |  86.1 KiB |  00m00s
[28/80] perl-podlators-1:6.0.2-521.fc44 100% |   6.3 MiB/s | 128.5 KiB |  00m00s
[29/80] perl-mro-0:1.29-521.fc44.x86_64 100% |   1.4 MiB/s |  29.5 KiB |  00m00s
[30/80] perl-overloading-0:0.02-521.fc4 100% | 628.1 KiB/s |  12.6 KiB |  00m00s
[31/80] perl-DynaLoader-0:1.57-521.fc44 100% |   1.3 MiB/s |  25.7 KiB |  00m00s
[32/80] groff-base-0:1.23.0-12.fc44.x86 100% |  44.9 MiB/s |   1.1 MiB |  00m00s
[33/80] perl-Fcntl-0:1.20-521.fc44.x86_ 100% |   1.1 MiB/s |  29.3 KiB |  00m00s
[34/80] perl-File-Temp-1:0.231.200-2.fc 100% |   2.9 MiB/s |  59.6 KiB |  00m00s
[35/80] perl-HTTP-Tiny-0:0.092-2.fc44.n 100% |   2.8 MiB/s |  57.2 KiB |  00m00s
[36/80] perl-IO-0:1.55-521.fc44.x86_64  100% |   4.0 MiB/s |  81.8 KiB |  00m00s
[37/80] perl-IPC-Open3-0:1.24-521.fc44. 100% |   1.2 MiB/s |  23.6 KiB |  00m00s
[38/80] perl-Pod-Simple-1:3.47-4.fc44.n 100% |  10.2 MiB/s | 220.0 KiB |  00m00s
[39/80] perl-Symbol-0:1.09-521.fc44.noa 100% | 659.9 KiB/s |  13.9 KiB |  00m00s
[40/80] perl-parent-1:0.244-521.fc44.no 100% | 744.0 KiB/s |  14.9 KiB |  00m00s
[41/80] perl-vars-0:1.05-521.fc44.noarc 100% | 632.0 KiB/s |  12.6 KiB |  00m00s
[42/80] perl-POSIX-0:2.23-521.fc44.x86_ 100% |   4.8 MiB/s |  97.6 KiB |  00m00s
[43/80] perl-Term-ANSIColor-0:5.01-522. 100% |   2.3 MiB/s |  47.7 KiB |  00m00s
[44/80] perl-Term-Cap-0:1.18-521.fc44.n 100% |   1.0 MiB/s |  22.0 KiB |  00m00s
[45/80] perl-File-Path-0:2.18-522.fc44. 100% |   1.6 MiB/s |  35.3 KiB |  00m00s
[46/80] perl-IO-Socket-SSL-0:2.098-2.fc 100% |  10.9 MiB/s | 234.7 KiB |  00m00s
[47/80] perl-MIME-Base64-0:3.16-521.fc4 100% |   1.4 MiB/s |  29.8 KiB |  00m00s
[48/80] perl-Net-SSLeay-0:1.94-12.fc44. 100% |  17.4 MiB/s | 373.4 KiB |  00m00s
[49/80] perl-Socket-4:2.040-3.fc44.x86_ 100% |   2.5 MiB/s |  55.3 KiB |  00m00s
[50/80] perl-Time-HiRes-4:1.9778-521.fc 100% |   2.8 MiB/s |  57.2 KiB |  00m00s
[51/80] perl-Time-Local-2:1.350-521.fc4 100% |   1.7 MiB/s |  34.5 KiB |  00m00s
[52/80] perl-File-stat-0:1.14-521.fc44. 100% | 836.2 KiB/s |  16.7 KiB |  00m00s
[53/80] perl-SelectSaver-0:1.02-521.fc4 100% | 569.2 KiB/s |  11.4 KiB |  00m00s
[54/80] perl-Pod-Escapes-1:1.07-521.fc4 100% | 989.6 KiB/s |  19.8 KiB |  00m00s
[55/80] perl-Text-Tabs+Wrap-0:2024.001- 100% |   1.1 MiB/s |  21.8 KiB |  00m00s
[56/80] perl-if-0:0.61.000-521.fc44.noa 100% | 683.2 KiB/s |  13.7 KiB |  00m00s
[57/80] perl-locale-0:1.13-521.fc44.noa 100% | 658.1 KiB/s |  13.2 KiB |  00m00s
[58/80] ncurses-0:6.5-9.20250614.fc44.x 100% |  19.0 MiB/s | 427.6 KiB |  00m00s
[59/80] perl-IO-Socket-IP-0:0.43-522.fc 100% |   1.9 MiB/s |  42.2 KiB |  00m00s
[60/80] perl-URI-0:5.34-3.fc44.noarch   100% |   7.3 MiB/s | 149.2 KiB |  00m00s
[61/80] perl-AutoLoader-0:5.74-521.fc44 100% |   1.0 MiB/s |  20.9 KiB |  00m00s
[62/80] perl-Class-Struct-0:0.68-521.fc 100% |   1.1 MiB/s |  21.7 KiB |  00m00s
[63/80] perl-Data-Dumper-0:2.191-522.fc 100% |   2.8 MiB/s |  56.5 KiB |  00m00s
[64/80] perl-MIME-Base32-0:1.303-25.fc4 100% |   1.0 MiB/s |  20.5 KiB |  00m00s
[65/80] perl-libnet-0:3.15-522.fc44.noa 100% |   6.3 MiB/s | 128.4 KiB |  00m00s
[66/80] perl-B-0:1.89-521.fc44.x86_64   100% |   8.7 MiB/s | 177.6 KiB |  00m00s
[67/80] perl-Digest-MD5-0:2.59-521.fc44 100% |   1.7 MiB/s |  36.0 KiB |  00m00s
[68/80] perl-FileHandle-0:2.05-521.fc44 100% | 757.9 KiB/s |  15.2 KiB |  00m00s
[69/80] perl-Digest-0:1.20-521.fc44.noa 100% |   1.2 MiB/s |  24.9 KiB |  00m00s
[70/80] perl-Encode-4:3.21-521.fc44.x86 100% |  42.1 MiB/s |   1.1 MiB |  00m00s
[71/80] perl-Getopt-Std-0:1.14-521.fc44 100% | 614.0 KiB/s |  15.3 KiB |  00m00s
[72/80] perl-Storable-1:3.37-522.fc44.x 100% |   4.7 MiB/s | 100.9 KiB |  00m00s
[73/80] glibc-devel-0:2.42.9000-25.fc44 100% |  26.0 MiB/s | 612.1 KiB |  00m00s
[74/80] libxcrypt-devel-0:4.5.2-3.fc44. 100% |   1.5 MiB/s |  30.0 KiB |  00m00s
[75/80] libatomic-0:16.0.1-0.3.fc44.1.x 100% |   1.3 MiB/s |  34.0 KiB |  00m00s
[76/80] kernel-headers-0:6.19.0-0.rc6.4 100% |  61.8 MiB/s |   1.7 MiB |  00m00s
[77/80] annobin-plugin-gcc-0:13.05-3.fc 100% |  26.7 MiB/s | 683.1 KiB |  00m00s
[78/80] gcc-plugin-annobin-0:16.0.1-0.3 100% |   1.8 MiB/s |  37.8 KiB |  00m00s
[79/80] annobin-docs-0:13.05-3.fc44.noa 100% |   4.3 MiB/s |  88.9 KiB |  00m00s
[80/80] htslib-0:1.23-1.fc44.x86_64     100% | 683.6 KiB/s | 618.7 KiB |  00m01s
--------------------------------------------------------------------------------
[80/80] Total                           100% |  45.5 MiB/s |  71.7 MiB |  00m02s
Running transaction
[ 1/82] Verify package files            100% | 321.0   B/s |  80.0   B |  00m00s
[ 2/82] Prepare transaction             100% |   2.2 KiB/s |  80.0   B |  00m00s
[ 3/82] Installing htslib-0:1.23-1.fc44 100% | 271.4 MiB/s |   1.4 MiB |  00m00s
[ 4/82] Installing libmpc-0:1.3.1-9.fc4 100% | 158.2 MiB/s | 162.0 KiB |  00m00s
[ 5/82] Installing cpp-0:16.0.1-0.3.fc4 100% | 337.0 MiB/s |  42.1 MiB |  00m00s
[ 6/82] Installing annobin-docs-0:13.05 100% |  32.7 MiB/s | 100.3 KiB |  00m00s
[ 7/82] Installing kernel-headers-0:6.1 100% | 213.0 MiB/s |   7.0 MiB |  00m00s
[ 8/82] Installing glibc-devel-0:2.42.9 100% | 183.5 MiB/s |   2.4 MiB |  00m00s
[ 9/82] Installing libxcrypt-devel-0:4. 100% |  32.5 MiB/s |  33.3 KiB |  00m00s
[10/82] Installing libatomic-0:16.0.1-0 100% |   0.0   B/s |  46.4 KiB |  00m00s
[11/82] Installing ncurses-0:6.5-9.2025 100% |  30.0 MiB/s | 615.3 KiB |  00m00s
[12/82] Installing groff-base-0:1.23.0- 100% | 125.6 MiB/s |   3.9 MiB |  00m00s
[13/82] Installing perl-Digest-0:1.20-5 100% |  36.2 MiB/s |  37.1 KiB |  00m00s
[14/82] Installing perl-Digest-MD5-0:2. 100% |  60.0 MiB/s |  61.5 KiB |  00m00s
[15/82] Installing perl-FileHandle-0:2. 100% |   0.0   B/s |   9.8 KiB |  00m00s
[16/82] Installing perl-B-0:1.89-521.fc 100% | 246.4 MiB/s | 504.5 KiB |  00m00s
[17/82] Installing perl-libnet-0:3.15-5 100% | 143.9 MiB/s | 294.7 KiB |  00m00s
[18/82] Installing perl-Data-Dumper-0:2 100% | 114.7 MiB/s | 117.4 KiB |  00m00s
[19/82] Installing perl-MIME-Base32-0:1 100% |  31.4 MiB/s |  32.2 KiB |  00m00s
[20/82] Installing perl-URI-0:5.34-3.fc 100% | 137.6 MiB/s | 281.8 KiB |  00m00s
[21/82] Installing perl-IO-Socket-IP-0: 100% |  99.8 MiB/s | 102.2 KiB |  00m00s
[22/82] Installing perl-AutoLoader-0:5. 100% |   0.0   B/s |  21.0 KiB |  00m00s
[23/82] Installing perl-IO-Socket-SSL-0 100% | 355.3 MiB/s | 727.6 KiB |  00m00s
[24/82] Installing perl-Net-SSLeay-0:1. 100% | 269.4 MiB/s |   1.3 MiB |  00m00s
[25/82] Installing perl-locale-0:1.13-5 100% |   0.0   B/s |   6.5 KiB |  00m00s
[26/82] Installing perl-if-0:0.61.000-5 100% |   0.0   B/s |   6.2 KiB |  00m00s
[27/82] Installing perl-Text-Tabs+Wrap- 100% |   0.0   B/s |  23.9 KiB |  00m00s
[28/82] Installing perl-Pod-Escapes-1:1 100% |   0.0   B/s |  25.9 KiB |  00m00s
[29/82] Installing perl-Time-Local-2:1. 100% |  68.9 MiB/s |  70.6 KiB |  00m00s
[30/82] Installing perl-Time-HiRes-4:1. 100% | 114.9 MiB/s | 117.7 KiB |  00m00s
[31/82] Installing perl-File-Path-0:2.1 100% |   0.0   B/s |  64.5 KiB |  00m00s
[32/82] Installing perl-HTTP-Tiny-0:0.0 100% | 155.9 MiB/s | 159.7 KiB |  00m00s
[33/82] Installing perl-Pod-Simple-1:3. 100% | 280.7 MiB/s | 574.9 KiB |  00m00s
[34/82] Installing perl-Class-Struct-0: 100% |   0.0   B/s |  25.9 KiB |  00m00s
[35/82] Installing perl-IPC-Open3-0:1.2 100% |   0.0   B/s |  28.5 KiB |  00m00s
[36/82] Installing perl-File-Temp-1:0.2 100% | 161.6 MiB/s | 165.5 KiB |  00m00s
[37/82] Installing perl-POSIX-0:2.23-52 100% | 227.0 MiB/s | 232.5 KiB |  00m00s
[38/82] Installing perl-Term-Cap-0:1.18 100% |   0.0   B/s |  30.6 KiB |  00m00s
[39/82] Installing perl-Term-ANSIColor- 100% |  96.9 MiB/s |  99.2 KiB |  00m00s
[40/82] Installing perl-Pod-Perldoc-0:3 100% |  12.7 MiB/s | 169.2 KiB |  00m00s
[41/82] Installing perl-podlators-1:6.0 100% |  26.2 MiB/s | 321.4 KiB |  00m00s
[42/82] Installing perl-File-stat-0:1.1 100% |   0.0   B/s |  13.1 KiB |  00m00s
[43/82] Installing perl-SelectSaver-0:1 100% |   0.0   B/s |   2.6 KiB |  00m00s
[44/82] Installing perl-Socket-4:2.040- 100% | 119.3 MiB/s | 122.2 KiB |  00m00s
[45/82] Installing perl-Symbol-0:1.09-5 100% |   0.0   B/s |   7.3 KiB |  00m00s
[46/82] Installing perl-Pod-Usage-4:2.0 100% |   6.6 MiB/s |  87.9 KiB |  00m00s
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Warning: skipped OpenPGP checks for 3 packages from repository: copr_base
Complete!
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/samtools-1.23-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |   1.3 KiB/s |   1.5 KiB |  00m01s
 fedora                                 100% |  20.8 KiB/s |  26.4 KiB |  00m01s
Repositories loaded.
Package "gcc-16.0.1-0.3.fc44.1.x86_64" is already installed.
Package "htslib-devel-1.23-1.fc44.x86_64" is already installed.
Package "htslib-tools-1.23-1.fc44.x86_64" is already installed.
Package "make-1:4.4.1-12.fc44.x86_64" is already installed.
Package "ncurses-devel-6.5-9.20250614.fc44.x86_64" is already installed.
Package "perl-FindBin-1.54-521.fc44.noarch" is already installed.
Package "perl-Getopt-Long-1:2.58-521.fc44.noarch" is already installed.
Package "perl-lib-0.65-521.fc44.x86_64" is already installed.
Package "perl-interpreter-4:5.42.0-521.fc44.x86_64" is already installed.
Package "zlib-ng-compat-devel-2.3.2-3.fc44.x86_64" is already installed.

Nothing to do.
Finish: build setup for samtools-1.23-1.fc44.src.rpm
Start: rpmbuild samtools-1.23-1.fc44.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.M0Yzhj
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.aAInx2
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ cd /builddir/build/BUILD/samtools-1.23-build
+ rm -rf samtools-1.23
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.23.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd samtools-1.23
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ rm -f INSTALL
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.3Y38kl
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 samtools-1.23
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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' ./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};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.23/configure
+ diff -u ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ mv ./htslib-1.23/configure.backup ./htslib-1.23/configure
+ /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/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
+ 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};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 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/bin --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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' '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
checking for gawk... gawk
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 gcc option to enable large file support... none needed
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_aux.o bam_aux.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_index.o bam_index.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_cat.o bam_cat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_fastq.o bam_fastq.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_plcmd.o bam_plcmd.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_plbuf.o bam_plbuf.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_md.o bam_md.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o sam_view.o sam_view.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_reheader.o bam_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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_rmdup.o bam_rmdup.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_rmdupse.o bam_rmdupse.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.23"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h
echo '#define SAMTOOLS_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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer"' >> version.h
echo '#define SAMTOOLS_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  "' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_stat.o bam_stat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o cut_target.o cut_target.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o sample.o 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_mate.o bam_mate.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o coverage.o coverage.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam2depth.o bam2depth.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o padding.o padding.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o phase.o phase.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bedcov.o bedcov.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o faidx.o faidx.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o dict.o dict.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bamshuf.o bamshuf.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_flags.o bam_flags.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o stats_isize.o stats_isize.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_tview.o bam_tview.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_split.o bam_split.c
bam_split.c: In function ‘prep_sam_file’:
bam_split.c:379:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  379 |     char *dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
bam_split.c: In function ‘init’:
bam_split.c:641:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  641 |     char* dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_tview_curses.o bam_tview_curses.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_sort.o bam_sort.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_tview_html.o bam_tview_html.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_quickcheck.o bam_quickcheck.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_lpileup.o bam_lpileup.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_addrprg.o bam_addrprg.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o tmp_file.o tmp_file.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o stats.o stats.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_ampliconclip.o bam_ampliconclip.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_import.o bam_import.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_samples.o bam_samples.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o consensus_pileup.o consensus_pileup.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o amplicon_stats.o amplicon_stats.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_markdup.o bam_markdup.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o reference.o reference.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o reset.o reset.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o cram_size.o cram_size.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o sam_opts.o sam_opts.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_consensus.o bam_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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o sam_utils.o sam_utils.c
sam_utils.c: In function ‘auto_index’:
sam_utils.c:122:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  122 |     char *delim = strstr(fn, HTS_IDX_DELIM);
      |                   ^~~~~~
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam.o bam.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bam_checksum.o bam_checksum.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DMAQ_LONGREADS -I.  -I./lz4  -c -o misc/maq2sam-long.o misc/maq2sam.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o misc/maq2sam-short.o misc/maq2sam.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bedidx.o bedidx.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o misc/md5sum-lite.o misc/md5sum-lite.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o misc/md5fa.o misc/md5fa.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o misc/ace2sam.o misc/ace2sam.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/test.o test/test.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o misc/wgsim.o misc/wgsim.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o lz4/lz4.o lz4/lz4.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/split/test_count_rg.o test/split/test_count_rg.c
In file included from test/split/test_count_rg.c:27:
test/split/../../bam_split.c: In function ‘prep_sam_file’:
test/split/../../bam_split.c:379:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  379 |     char *dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
test/split/../../bam_split.c: In function ‘init’:
test/split/../../bam_split.c:641:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  641 |     char* dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
In file included from test/split/test_expand_format_string.c:27:
test/split/../../bam_split.c: In function ‘prep_sam_file’:
test/split/../../bam_split.c:379:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  379 |     char *dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
test/split/../../bam_split.c: In function ‘init’:
test/split/../../bam_split.c:641:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  641 |     char* dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/split/test_parse_args.o test/split/test_parse_args.c
In file included from test/split/test_parse_args.c:27:
test/split/../../bam_split.c: In function ‘prep_sam_file’:
test/split/../../bam_split.c:379:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  379 |     char *dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
test/split/../../bam_split.c: In function ‘init’:
test/split/../../bam_split.c:641:20: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  641 |     char* dirsep = strrchr(opts->merged_input_name, '/');
      |                    ^~~~~~~
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/vcf-miniview.o test/vcf-miniview.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o bamtk.o bamtk.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.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 misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -o misc/maq2sam-short misc/maq2sam-short.o -lz 
gcc  -L./lz4 -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 misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
gcc  -L./lz4 -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 misc/md5fa misc/md5fa.o -lhts -lz 
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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I.  -I./lz4  -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc  -L./lz4 -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/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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 misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc  -L./lz4 -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/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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 misc/wgsim misc/wgsim.o -lm -lhts -lz 
gcc  -L./lz4 -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/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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/vcf-miniview test/vcf-miniview.o -lhts -lz  -lpthread
gcc  -L./lz4 -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/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -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 samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz  -lpthread
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.5YdRRr
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ '[' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
++ dirname /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/samtools-1.23-build
+ mkdir /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 samtools-1.23
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/samtools-1.23-build/BUILDROOT 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin
/usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin
/usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/ace2sam /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/blast2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/bowtie2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/export2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/fasta-sanitize.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/interpolate_sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/maq2sam-long /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/maq2sam-short /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/md5fa /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/md5sum-lite /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/novo2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-ampliconstats /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-bamstats /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/psl2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/sam2vcf.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/samtools /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/samtools.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/seq_cache_populate.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/soap2sam.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/wgsim /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/wgsim_eval.pl /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.23-1.fc44 --unique-debug-suffix -1.23-1.fc44.x86_64 --unique-debug-src-base samtools-1.23-1.fc44.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.23-build/samtools-1.23
find-debuginfo: starting
Extracting debug info from 7 files
DWARF-compressing 7 files
sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/samtools-1.23-1.fc44.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ COMPRESS='gzip -9 -n'
+ COMPRESS_EXT=.gz
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /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
+ /usr/bin/add-det --brp -j4 /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
Scanned 16 directories and 148 files,
    processed 43 inodes,
    0 modified (0 replaced + 0 rewritten),
    0 unsupported format, 0 errors
+ /usr/bin/linkdupes --brp /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr
Scanned 15 directories and 148 files,
    considered 148 files, read 7 files, linked 0 files, 0 errors
    sum of sizes of linked files: 0 bytes
Reading /builddir/build/BUILD/samtools-1.23-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.nWfM1Y
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 samtools-1.23
+ ldd samtools
+ grep -E -e '/lib(64)?/libhts\.so\.' -e '/lib64/lp64d/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007fa77bbec000)
+ make test
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-}
test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

bgzip -c -b 65272 -s 5 /tmp/ZUKKp2UiXy/bgzip.dat.gz
.. ok

bgzip -c -b 979200 -s 6 /tmp/ZUKKp2UiXy/bgzip.dat.gz
.. ok

bgzip -c -b 652804 -s 6 /tmp/ZUKKp2UiXy/bgzip.dat.gz
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools faidx /tmp/ZUKKp2UiXy/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq.gz 3:11-13
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq.gz 1:100-104
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq 1:99998-100007
.. ok

.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fqidx /tmp/ZUKKp2UiXy/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/dict.fa
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/ZUKKp2UiXy/dict.fa.gz
.. ok

test_dict:
	cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools dict -AH < /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/dict.alias.fa
.. ok

test_dict:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools dict -H -l /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/dict.alt < /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/dict.alias.fa
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view /tmp/ZUKKp2UiXy/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view /tmp/ZUKKp2UiXy/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/ZUKKp2UiXy/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/ZUKKp2UiXy/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/ZUKKp2UiXy/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/ZUKKp2UiXy/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/ZUKKp2UiXy/auto_indexed.csi && cat /tmp/ZUKKp2UiXy/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/ZUKKp2UiXy/auto_indexed.crai && cat /tmp/ZUKKp2UiXy/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/ZUKKp2UiXy/auto_indexed.csi && cat /tmp/ZUKKp2UiXy/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 /tmp/ZUKKp2UiXy/large_chrom.bam ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 /tmp/ZUKKp2UiXy/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/ZUKKp2UiXy/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/ZUKKp2UiXy/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai /tmp/ZUKKp2UiXy/test_input_1_b.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /tmp/ZUKKp2UiXy/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 -M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam && cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam /tmp/ZUKKp2UiXy/auto_indexed.csi && cat /tmp/ZUKKp2UiXy/auto_indexed.csi
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.cram /tmp/ZUKKp2UiXy/auto_indexed.crai && cat /tmp/ZUKKp2UiXy/auto_indexed.crai
.. ok

test_index:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.sam /tmp/ZUKKp2UiXy/auto_indexed.csi && cat /tmp/ZUKKp2UiXy/auto_indexed.csi
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/ZUKKp2UiXy/mpileup.bam.list -f /tmp/ZUKKp2UiXy/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/ZUKKp2UiXy/mpileup.cram.list -f /tmp/ZUKKp2UiXy/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/ZUKKp2UiXy/mpileup.bam.urllist -f /tmp/ZUKKp2UiXy/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -b /tmp/ZUKKp2UiXy/mpileup.cram.urllist -f /tmp/ZUKKp2UiXy/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/ZUKKp2UiXy/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ZUKKp2UiXy/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup -B --ff 0x14 -f /tmp/ZUKKp2UiXy/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ZUKKp2UiXy/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools mpileup /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/mpileup/overlap.bam | grep 128814202
test/test.pl: no IO::Pty module or can't open pty; skipping usage tests
.. ok

test_usage:
	samtools
test_view:
	Generating test data file .................. done
	1: SAM -> BAM -> SAM                                        .. ok

	2: SAM -> uncompressed BAM                                  .. ok

	3: uncompressed BAM -> SAM and compare                      .. ok

	4: SAM -> fast compressed BAM                               .. ok

	5: fast compressed BAM -> SAM and compare                   .. ok

	6: SAM -> CRAM -> SAM (UR header tags)                      .. ok

	7: SAM -> CRAM -> SAM (M5 header tags)                      .. ok

	8: BAM -> CRAM with UR -> SAM                               .. ok

	9: SAM -> BAM (M5 header tags)                              .. ok

	10: SAM -> BAM -> CRAM -> SAM (M5 header tags)              .. ok

	11: CRAM -> BAM with UR                                     .. ok

	12: CRAM -> BAM with M5                                     .. ok

	13: SAM -> SAM via stdout                                   .. ok

	14: SAM -> BAM via stdout                                   .. ok

	15: SAM -> CRAM via stdout                                  .. ok

	16: SAM from stdin -> SAM                                   .. ok

	17: BAM from stdin -> SAM                                   .. ok

	18: CRAM from stdin -> SAM                                  .. ok

	19: samtools view -H (SAM input)                            .. ok

	20: samtools view -H (BAM input)                            .. ok

	21: samtools view -H (CRAM input)                           .. ok

	22: No headers (SAM input)                                  .. ok

	23: No headers (BAM input)                                  .. ok

	24: No headers (CRAM input)                                 .. ok

	25: Filter -f 128 (SAM input)                               .. ok

	26: Count -f 128 (SAM input)                                .. ok

	27: Filter -f 128 (BAM input)                               .. ok

	28: Count -f 128 (BAM input)                                .. ok

	29: Filter -f 128 (CRAM input)                              .. ok

	30: Count -f 128 (CRAM input)                               .. ok

	31: Filter -F 128 (SAM input)                               .. ok

	32: Count -F 128 (SAM input)                                .. ok

	33: Filter -F 128 (BAM input)                               .. ok

	34: Count -F 128 (BAM input)                                .. ok

	35: Filter -F 128 (CRAM input)                              .. ok

	36: Count -F 128 (CRAM input)                               .. ok

	37: Filter -F 128 -f 2 (SAM input)                          .. ok

	38: Count -F 128 -f 2 (SAM input)                           .. ok

	39: Filter -F 128 -f 2 (BAM input)                          .. ok

	40: Count -F 128 -f 2 (BAM input)                           .. ok

	41: Filter -F 128 -f 2 (CRAM input)                         .. ok

	42: Count -F 128 -f 2 (CRAM input)                          .. ok

	43: Filter -r grp2 (SAM input)                              .. ok

	44: Count -r grp2 (SAM input)                               .. ok

	45: Filter -r grp2 (BAM input)                              .. ok

	46: Count -r grp2 (BAM input)                               .. ok

	47: Filter -r grp2 (CRAM input)                             .. ok

	48: Count -r grp2 (CRAM input)                              .. ok

	49: Filter -R /tmp/ZUKKp2UiXy/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/ZUKKp2UiXy/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/ZUKKp2UiXy/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/ZUKKp2UiXy/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/ZUKKp2UiXy/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/ZUKKp2UiXy/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/ZUKKp2UiXy/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/ZUKKp2UiXy/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/ZUKKp2UiXy/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/ZUKKp2UiXy/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/ZUKKp2UiXy/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/ZUKKp2UiXy/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/ZUKKp2UiXy/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/ZUKKp2UiXy/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/ZUKKp2UiXy/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/ZUKKp2UiXy/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/ZUKKp2UiXy/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/ZUKKp2UiXy/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/ZUKKp2UiXy/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/ZUKKp2UiXy/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/ZUKKp2UiXy/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/ZUKKp2UiXy/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/ZUKKp2UiXy/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/ZUKKp2UiXy/view.001.forn (CRAM input)     .. ok

	73: Filter -d BC (SAM input)                                .. ok

	74: Count -d BC (SAM input)                                 .. ok

	75: Filter -d BC (BAM input)                                .. ok

	76: Count -d BC (BAM input)                                 .. ok

	77: Filter -d BC (CRAM input)                               .. ok

	78: Count -d BC (CRAM input)                                .. ok

	79: Filter -d BC:TGCA (SAM input)                           .. ok

	80: Count -d BC:TGCA (SAM input)                            .. ok

	81: Filter -d BC:TGCA (BAM input)                           .. ok

	82: Count -d BC:TGCA (BAM input)                            .. ok

	83: Filter -d BC:TGCA (CRAM input)                          .. ok

	84: Count -d BC:TGCA (CRAM input)                           .. ok

	85: Filter -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/ZUKKp2UiXy/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/ZUKKp2UiXy/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/ZUKKp2UiXy/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/ZUKKp2UiXy/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/ZUKKp2UiXy/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/ZUKKp2UiXy/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/ZUKKp2UiXy/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/ZUKKp2UiXy/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/ZUKKp2UiXy/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/ZUKKp2UiXy/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/ZUKKp2UiXy/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/ZUKKp2UiXy/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/ZUKKp2UiXy/view.001.fogn (CRAM input) .. ok

	109: Filter -d NE:TGCA (SAM input)                          .. ok

	110: Count -d NE:TGCA (SAM input)                           .. ok

	111: Filter -d NE:TGCA (BAM input)                          .. ok

	112: Count -d NE:TGCA (BAM input)                           .. ok

	113: Filter -d NE:TGCA (CRAM input)                         .. ok

	114: Count -d NE:TGCA (CRAM input)                          .. ok

	115: Filter -d TGCA (SAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test115.sam -h -d TGCA /tmp/ZUKKp2UiXy/view.001.sam --no-PG


.. expected failure

	116: Count -d TGCA (SAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -d TGCA /tmp/ZUKKp2UiXy/view.001.sam --no-PG


.. expected failure

	117: Filter -d TGCA (BAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test117.sam -h -d TGCA /tmp/ZUKKp2UiXy/view.test001.bam --no-PG


.. expected failure

	118: Count -d TGCA (BAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -d TGCA /tmp/ZUKKp2UiXy/view.test001.bam --no-PG


.. expected failure

	119: Filter -d TGCA (CRAM input)                            samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test119.sam -h -d TGCA /tmp/ZUKKp2UiXy/view.test006.cram --no-PG


.. expected failure

	120: Count -d TGCA (CRAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -d TGCA /tmp/ZUKKp2UiXy/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ZUKKp2UiXy/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test121.sam -h -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc /tmp/ZUKKp2UiXy/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ZUKKp2UiXy/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc /tmp/ZUKKp2UiXy/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ZUKKp2UiXy/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test123.sam -h -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc /tmp/ZUKKp2UiXy/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ZUKKp2UiXy/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc /tmp/ZUKKp2UiXy/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ZUKKp2UiXy/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test125.sam -h -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc /tmp/ZUKKp2UiXy/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/ZUKKp2UiXy/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -D BClong:/tmp/ZUKKp2UiXy/view.001.fobc /tmp/ZUKKp2UiXy/view.test006.cram --no-PG


.. expected failure

	127: Filter -d BC:ACGT -d RG:grp2 (SAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/ZUKKp2UiXy/view.001.sam --no-PG


.. expected failure

	128: Count -d BC:ACGT -d RG:grp2 (SAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/ZUKKp2UiXy/view.001.sam --no-PG


.. expected failure

	129: Filter -d BC:ACGT -d RG:grp2 (BAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/ZUKKp2UiXy/view.test001.bam --no-PG


.. expected failure

	130: Count -d BC:ACGT -d RG:grp2 (BAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/ZUKKp2UiXy/view.test001.bam --no-PG


.. expected failure

	131: Filter -d BC:ACGT -d RG:grp2 (CRAM input)              samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -o /tmp/ZUKKp2UiXy/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/ZUKKp2UiXy/view.test006.cram --no-PG


.. expected failure

	132: Count -d BC:ACGT -d RG:grp2 (CRAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/ZUKKp2UiXy/view.test006.cram --no-PG


.. expected failure

	133: Filter -d NM:13 (SAM input)                            .. ok

	134: Count -d NM:13 (SAM input)                             .. ok

	135: Filter -d NM:13 (BAM input)                            .. ok

	136: Count -d NM:13 (BAM input)                             .. ok

	137: Filter -d NM:13 (CRAM input)                           .. ok

	138: Count -d NM:13 (CRAM input)                            .. ok

	139: Filter -d ab:z (SAM input)                             .. ok

	140: Count -d ab:z (SAM input)                              .. ok

	141: Filter -d ab:z (BAM input)                             .. ok

	142: Count -d ab:z (BAM input)                              .. ok

	143: Filter -d ab:z (CRAM input)                            .. ok

	144: Count -d ab:z (CRAM input)                             .. ok

	145: Filter -l Library 2 (SAM input)                        .. ok

	146: Count -l Library 2 (SAM input)                         .. ok

	147: Filter -l Library 2 (BAM input)                        .. ok

	148: Count -l Library 2 (BAM input)                         .. ok

	149: Filter -l Library 2 (CRAM input)                       .. ok

	150: Count -l Library 2 (CRAM input)                        .. ok

	151: Filter -l Library 3 (SAM input)                        .. ok

	152: Count -l Library 3 (SAM input)                         .. ok

	153: Filter -l Library 3 (BAM input)                        .. ok

	154: Count -l Library 3 (BAM input)                         .. ok

	155: Filter -l Library 3 (CRAM input)                       .. ok

	156: Count -l Library 3 (CRAM input)                        .. ok

	157: Filter -q 50 (SAM input)                               .. ok

	158: Count -q 50 (SAM input)                                .. ok

	159: Filter -q 50 (BAM input)                               .. ok

	160: Count -q 50 (BAM input)                                .. ok

	161: Filter -q 50 (CRAM input)                              .. ok

	162: Count -q 50 (CRAM input)                               .. ok

	163: Filter -q 99 (SAM input)                               .. ok

	164: Count -q 99 (SAM input)                                .. ok

	165: Filter -q 99 (BAM input)                               .. ok

	166: Count -q 99 (BAM input)                                .. ok

	167: Filter -q 99 (CRAM input)                              .. ok

	168: Count -q 99 (CRAM input)                               .. ok

	169: Filter -q 100 (SAM input)                              .. ok

	170: Count -q 100 (SAM input)                               .. ok

	171: Filter -q 100 (BAM input)                              .. ok

	172: Count -q 100 (BAM input)                               .. ok

	173: Filter -q 100 (CRAM input)                             .. ok

	174: Count -q 100 (CRAM input)                              .. ok

	175: Filter -x fa (SAM input)                               .. ok

	176: Count -x fa (SAM input)                                .. ok

	177: Filter -x fa (BAM input)                               .. ok

	178: Count -x fa (BAM input)                                .. ok

	179: Filter -x fa (CRAM input)                              .. ok

	180: Count -x fa (CRAM input)                               .. ok

	181: Filter -x fa -x ha (SAM input)                         .. ok

	182: Count -x fa -x ha (SAM input)                          .. ok

	183: Filter -x fa -x ha (BAM input)                         .. ok

	184: Count -x fa -x ha (BAM input)                          .. ok

	185: Filter -x fa -x ha (CRAM input)                        .. ok

	186: Count -x fa -x ha (CRAM input)                         .. ok

	187: Filter -x fa,ha (SAM input)                            .. ok

	188: Count -x fa,ha (SAM input)                             .. ok

	189: Filter -x fa,ha (BAM input)                            .. ok

	190: Count -x fa,ha (BAM input)                             .. ok

	191: Filter -x fa,ha (CRAM input)                           .. ok

	192: Count -x fa,ha (CRAM input)                            .. ok

	193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	205: Filter -x fa -r grp2 (SAM input)                       .. ok

	206: Count -x fa -r grp2 (SAM input)                        .. ok

	207: Filter -x fa -r grp2 (BAM input)                       .. ok

	208: Count -x fa -r grp2 (BAM input)                        .. ok

	209: Filter -x fa -r grp2 (CRAM input)                      .. ok

	210: Count -x fa -r grp2 (CRAM input)                       .. ok

	211: Filter -x RG -r grp2 (SAM input)                       .. ok

	212: Count -x RG -r grp2 (SAM input)                        .. ok

	213: Filter -x RG -r grp2 (BAM input)                       .. ok

	214: Count -x RG -r grp2 (BAM input)                        .. ok

	215: Filter -x RG -r grp2 (CRAM input)                      .. ok

	216: Count -x RG -r grp2 (CRAM input)                       .. ok

	217: Filter -m 10 (SAM input)                               .. ok

	218: Count -m 10 (SAM input)                                .. ok

	219: Filter -m 10 (BAM input)                               .. ok

	220: Count -m 10 (BAM input)                                .. ok

	221: Filter -m 10 (CRAM input)                              .. ok

	222: Count -m 10 (CRAM input)                               .. ok

	223: Filter -m 11 (SAM input)                               .. ok

	224: Count -m 11 (SAM input)                                .. ok

	225: Filter -m 11 (BAM input)                               .. ok

	226: Count -m 11 (BAM input)                                .. ok

	227: Filter -m 11 (CRAM input)                              .. ok

	228: Count -m 11 (CRAM input)                               .. ok

	229: Filter -m 15 (SAM input)                               .. ok

	230: Count -m 15 (SAM input)                                .. ok

	231: Filter -m 15 (BAM input)                               .. ok

	232: Count -m 15 (BAM input)                                .. ok

	233: Filter -m 15 (CRAM input)                              .. ok

	234: Count -m 15 (CRAM input)                               .. ok

	235: Filter -m 16 (SAM input)                               .. ok

	236: Count -m 16 (SAM input)                                .. ok

	237: Filter -m 16 (BAM input)                               .. ok

	238: Count -m 16 (BAM input)                                .. ok

	239: Filter -m 16 (CRAM input)                              .. ok

	240: Count -m 16 (CRAM input)                               .. ok

	241: Filter -e !(flag & 128) && (flag & 2) (SAM input)      .. ok

	242: Count -e !(flag & 128) && (flag & 2) (SAM input)       .. ok

	243: Filter -e !(flag & 128) && (flag & 2) (BAM input)      .. ok

	244: Count -e !(flag & 128) && (flag & 2) (BAM input)       .. ok

	245: Filter -e !(flag & 128) && (flag & 2) (CRAM input)     .. ok

	246: Count -e !(flag & 128) && (flag & 2) (CRAM input)      .. ok

	247: Filter -e [BC] (SAM input)                             .. ok

	248: Count -e [BC] (SAM input)                              .. ok

	249: Filter -e [BC] (BAM input)                             .. ok

	250: Count -e [BC] (BAM input)                              .. ok

	251: Filter -e [BC] (CRAM input)                            .. ok

	252: Count -e [BC] (CRAM input)                             .. ok

	253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	259: Filter -e mapq >= 50 (SAM input)                       .. ok

	260: Count -e mapq >= 50 (SAM input)                        .. ok

	261: Filter -e mapq >= 50 (BAM input)                       .. ok

	262: Count -e mapq >= 50 (BAM input)                        .. ok

	263: Filter -e mapq >= 50 (CRAM input)                      .. ok

	264: Count -e mapq >= 50 (CRAM input)                       .. ok

	265: Filter -e mapq >= 99 (SAM input)                       .. ok

	266: Count -e mapq >= 99 (SAM input)                        .. ok

	267: Filter -e mapq >= 99 (BAM input)                       .. ok

	268: Count -e mapq >= 99 (BAM input)                        .. ok

	269: Filter -e mapq >= 99 (CRAM input)                      .. ok

	270: Count -e mapq >= 99 (CRAM input)                       .. ok

	271: Filter -e mapq >= 100 (SAM input)                      .. ok

	272: Count -e mapq >= 100 (SAM input)                       .. ok

	273: Filter -e mapq >= 100 (BAM input)                      .. ok

	274: Count -e mapq >= 100 (BAM input)                       .. ok

	275: Filter -e mapq >= 100 (CRAM input)                     .. ok

	276: Count -e mapq >= 100 (CRAM input)                      .. ok

	277: 1bp reads file SAM -> BAM -> SAM                       .. ok

	278: 1bp reads file SAM -> CRAM -> SAM                      .. ok

	278: Region  Z (BAM input)                                  .. ok

	279: Count  Z (BAM input)                                   .. ok

	280: Region  Z (CRAM input)                                 .. ok

	281: Count  Z (CRAM input)                                  .. ok

	282: Region  Z:30 (BAM input)                               .. ok

	283: Count  Z:30 (BAM input)                                .. ok

	284: Region  Z:30 (CRAM input)                              .. ok

	285: Count  Z:30 (CRAM input)                               .. ok

	286: Region  Z:20-40 (BAM input)                            .. ok

	287: Count  Z:20-40 (BAM input)                             .. ok

	288: Region  Z:20-40 (CRAM input)                           .. ok

	289: Count  Z:20-40 (CRAM input)                            .. ok

	290: Region  ref1 (BAM input)                               .. ok

	291: Count  ref1 (BAM input)                                .. ok

	292: Region  ref1 (CRAM input)                              .. ok

	293: Count  ref1 (CRAM input)                               .. ok

	294: Region  ref1:15 (BAM input)                            .. ok

	295: Count  ref1:15 (BAM input)                             .. ok

	296: Region  ref1:15 (CRAM input)                           .. ok

	297: Count  ref1:15 (CRAM input)                            .. ok

	298: Region  ref1:15-45 (BAM input)                         .. ok

	299: Count  ref1:15-45 (BAM input)                          .. ok

	300: Region  ref1:15-45 (CRAM input)                        .. ok

	301: Count  ref1:15-45 (CRAM input)                         .. ok

	302: Region  ref1:15-45 ref2 (BAM input)                    .. ok

	303: Count  ref1:15-45 ref2 (BAM input)                     .. ok

	304: Region  ref1:15-45 ref2 (CRAM input)                   .. ok

	305: Count  ref1:15-45 ref2 (CRAM input)                    .. ok

	306: Region  ref1:15-45 ref2:16 (BAM input)                 .. ok

	307: Count  ref1:15-45 ref2:16 (BAM input)                  .. ok

	308: Region  ref1:15-45 ref2:16 (CRAM input)                .. ok

	309: Count  ref1:15-45 ref2:16 (CRAM input)                 .. ok

	310: Region  ref1:15-45 ref2:16-31 (BAM input)              .. ok

	311: Count  ref1:15-45 ref2:16-31 (BAM input)               .. ok

	312: Region  ref1:15-45 ref2:16-31 (CRAM input)             .. ok

	313: Count  ref1:15-45 ref2:16-31 (CRAM input)              .. ok

	314: Region  ref1:15-15 ref1:45-45 (BAM input)              .. ok

	315: Count  ref1:15-15 ref1:45-45 (BAM input)               .. ok

	316: Region  ref1:15-15 ref1:45-45 (CRAM input)             .. ok

	317: Count  ref1:15-15 ref1:45-45 (CRAM input)              .. ok

	318: Region -f 128 ref1 (BAM input)                         .. ok

	319: Count -f 128 ref1 (BAM input)                          .. ok

	320: Region -f 128 ref1 (CRAM input)                        .. ok

	321: Count -f 128 ref1 (CRAM input)                         .. ok

	322: Region -q 50 ref1:15-45 (BAM input)                    .. ok

	323: Count -q 50 ref1:15-45 (BAM input)                     .. ok

	324: Region -q 50 ref1:15-45 (CRAM input)                   .. ok

	325: Count -q 50 ref1:15-45 (CRAM input)                    .. ok

	326: Region -r grp2 ref1:15-45 (BAM input)                  .. ok

	327: Count -r grp2 ref1:15-45 (BAM input)                   .. ok

	328: Region -r grp2 ref1:15-45 (CRAM input)                 .. ok

	329: Count -r grp2 ref1:15-45 (CRAM input)                  .. ok

	330: Region  * (BAM input)                                  .. ok

	331: Count  * (BAM input)                                   .. ok

	332: Region  * (CRAM input)                                 .. ok

	333: Count  * (CRAM input)                                  .. ok

	334: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed  (BAM input).. ok

	335: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed  (BAM input).. ok

	336: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed  (CRAM input).. ok

	337: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed  (CRAM input).. ok

	338: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.02.bed  (BAM input).. ok

	339: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.02.bed  (BAM input).. ok

	340: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.02.bed  (CRAM input).. ok

	341: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.02.bed  (CRAM input).. ok

	342: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed  (BAM input).. ok

	343: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed  (BAM input).. ok

	344: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed  (CRAM input).. ok

	345: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed  (CRAM input).. ok

	346: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.02.bed  (BAM input).. ok

	347: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.02.bed  (BAM input).. ok

	348: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.02.bed  (CRAM input).. ok

	349: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.02.bed  (CRAM input).. ok

	350: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.03.bed  (BAM input).. ok

	351: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.03.bed  (BAM input).. ok

	352: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.03.bed  (CRAM input).. ok

	353: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.03.bed  (CRAM input).. ok

	354: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok

	355: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z (BAM input).. ok

	356: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok

	357: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z (CRAM input).. ok

	358: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	359: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	360: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	361: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	362: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	363: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	364: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	365: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	366: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	367: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	368: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	369: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	370: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	371: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	372: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	373: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	374: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok

	375: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref2 (BAM input).. ok

	376: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	377: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	378: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	379: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	380: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	381: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	382: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	383: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	384: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	385: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	386: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	387: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	388: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	389: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	390: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	391: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	392: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	393: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	394: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	395: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	396: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	397: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	398: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	399: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	400: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	401: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	402: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	403: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	404: Region -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	405: Count -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	406: -L with nested regions                                 .. ok

	407: Make BAM with no M5/UR tags                            .. ok

	408: Add @SQ with -t (SAM -> SAM)                           .. ok

	409: Add @SQ with -T (SAM -> SAM)                           .. ok

	410: Add @SQ with -t (BAM -> SAM)                           .. ok

	411: Add @SQ with -T (BAM -> SAM)                           .. ok

	412: Add @SQ with -t (SAM -> BAM)                           .. ok

	413: Add @SQ with -T (SAM -> BAM)                           .. ok

	414: Add @SQ with -t (BAM -> BAM)                           .. ok

	415: Add @SQ with -T (BAM -> BAM)                           .. ok

	416: Add @SQ with -t (SAM -> CRAM)                          .. ok

	417: Add @SQ with -T (SAM -> CRAM)                          .. ok

	418: Add @SQ with -t (BAM -> CRAM)                          .. ok

	419: Add @SQ with -T (BAM -> CRAM)                          .. ok

	420: Make CRAM with no UR field                             .. ok

	421: Decoding CRAM with no UR field via -T                  .. ok

	422: CIGAR B-operator removal                               .. ok

	423: Big SAM -> BAM                                         .. ok

	424: Big SAM -> BAM (2 threads)                             .. ok

	425: Big SAM -> BAM (4 threads)                             .. ok

	426: Big SAM -> CRAM                                        .. ok

	427: Big SAM -> CRAM (2 threads)                            .. ok

	428: Big SAM -> CRAM (4 threads)                            .. ok

	429: Subsample 0.2 (SAM input) ............ ok

	430: Subsample 0.5 (SAM input) ............ ok

	431: Subsample 0.8 (SAM input) ............ ok

	432: Subsample 0.2 (BAM input) ............ ok

	433: Subsample 0.5 (BAM input) ............ ok

	434: Subsample 0.8 (BAM input) ............ ok

	435: Subsample 0.2 (CRAM input) ............ ok

	436: Subsample 0.5 (CRAM input) ............ ok

	437: Subsample 0.8 (CRAM input) ............ ok

	438: SAM add PG                                             .. ok

	439: Unset dup flag, remove dt and do tags                  .. ok

	440: Unmap dup flagged reads.                               .. ok

	441: Unmap dup flagged reads.                               .. ok

	442: fetch pairs                                            .. ok

	443: fetch pairs                                            .. ok

	444: fetch pairs                                            .. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 5 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 29 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 30 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -n 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -n 1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -n 5 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_head:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.sam
.. ok

test_cat:
	Generating test data file .................. done
	Generate BAM file #1                                        .. ok

	Generate BAM region file #1                                 .. ok

	Generate CRAM file #1                                       .. ok

	Generating test data file .................. done
	Generate BAM file #2                                        .. ok

	Generate BAM region file #2                                 .. ok

	Generate CRAM file #2                                       .. ok

	Generating test data file .................. done
	Generate BAM file #3                                        .. ok

	Generate BAM region file #3                                 .. ok

	Generate CRAM file #3                                       .. ok

	Generating test data file .................. done
	Generate BAM file #4                                        .. ok

	Generate BAM region file #4                                 .. ok

	Generate CRAM file #4                                       .. ok

	1: cat BAM files                                            .. ok

	2: cat recompressed BAM files                               .. ok

	3: cat CRAM files                                           .. ok

	4: cat CRAM subregion files                                 .. ok

	5: cat BAM files to stdout                                  .. ok

	6: cat recompressed BAM files to stdout                     .. ok

	7: cat CRAM files to stdout                                 .. ok

	8: cat CRAM subregion files to stdout                       .. ok

	9: cat CRAM part 1/2                                        .. ok

	9: cat CRAM part 2/2                                        .. ok

	9: cat CRAM parts 1/2 + 2/2                                 .. ok

	10: cat BAM files with new header                           .. ok

	11: cat recompressed BAM files with new header              .. ok

	12: cat CRAM files with new header                          .. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/0.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -s test/bam2fq/1.1.fq.expected  | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/0.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -s test/bam2fq/5.s.fq.expected  | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG	ID:rgid'
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/import/2.interleaved.fq -T ""
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/import/3.interleaved.fq -i
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T "*"
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T ""
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -U test/bam2fq/UMI.fq.expected
.. ok

test_import:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools import --no-PG -U --UMI-tag OX test/bam2fq/UMI.fq.expected
.. ok

test_bam2fq:
	Generate BAM file                                           .. ok

	Generate CRAM file                                          .. ok

	1: fastq  (SAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input)                                      [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input)                                    [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -t -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fasta  -N -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -s /tmp/ZUKKp2UiXy/bam2fq.discard.s.fq -0 /tmp/ZUKKp2UiXy/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -T '' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -t -T '*' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -O --no-sc /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq  -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam
.. ok

test_bam2fq:
	Generate BAM file (2 threads)                               .. ok

	Generate CRAM file (2 threads)                              .. ok

	1: fastq  (SAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input) (2 threads)                          [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input) (2 threads)                        [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i.fq -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/s.fq -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/1.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/2.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fq -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fa -2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/o.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -s /tmp/ZUKKp2UiXy/bam2fq.discard.s.fq -0 /tmp/ZUKKp2UiXy/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/i2.fq -0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/0.fq /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -T '' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -t -T '*' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d MD:10 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d NM:0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -N -T '*' -d ia /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -d NM:13 -d NM:14 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -O --no-sc --no-sc-bkp -T 's0' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -O --no-sc -T's0' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -O --no-sc /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -@ 2 -O --no-sc --sc-aux s1 -T's0,s1' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/bam2fq.sc.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -U test/import/UMI.expected.sam
.. ok

test_bam2fq:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fastq -U --UMI-tag RX,OX test/import/UMI-OX.expected.sam
.. ok

test_depad:
	Generate BAM file                                           .. ok

	depad  (SAM input)                                          .. ok

	depad -s (SAM input)                                        .. ok

	depad -u (SAM input)                                        .. ok

	depad -1 (SAM input)                                        .. ok

	depad  (BAM input)                                          .. ok

	depad -s (BAM input)                                        .. ok

	depad -u (BAM input)                                        .. ok

	depad -1 (BAM input)                                        .. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/7_supp.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/7_supp_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/8_secondary.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/8_secondary_large.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/10_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -g 4 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4

	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -I s1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -I Sample /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/mpileup/ce.fa /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/15.big_del.sam | tail -n+4
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test.fa

	ERR: [E::faidx_adjust_position] The sequence "ref1" was not found
Failed to fetch the sequence "ref1"

.. expected failure

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test1.fa | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats --ref-stats-chunk -1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test1.fa | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test1.fa alpha:10-20 | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.sam -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11.stats.targets  | grep -e"^RFS"
.. ok

test_stats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools stats --ref-stats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11_target.bam -r /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/test1.fa -t /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/stat/11.stats.targets ref1 | grep -e"^RFS"
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -O sam -b /tmp/3sW3LEKQZL - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/ZUKKp2UiXy/merge.tag.1.bam /tmp/ZUKKp2UiXy/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/ZUKKp2UiXy/merge.tag.3.bam /tmp/ZUKKp2UiXy/merge.tag.4.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/merge.bed - /tmp/ZUKKp2UiXy/merge.bed.1.bam /tmp/ZUKKp2UiXy/merge.bed.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_template_coordinate.2.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -O sam -b /tmp/vaVNAvAsUh - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/ZUKKp2UiXy/merge.tag.1.bam /tmp/ZUKKp2UiXy/merge.tag.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/ZUKKp2UiXy/merge.tag.3.bam /tmp/ZUKKp2UiXy/merge.tag.4.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/merge.bed - /tmp/ZUKKp2UiXy/merge.bed.1.bam /tmp/ZUKKp2UiXy/merge.bed.2.bam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 --no-PG -r -O SAM - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_template_coordinate.1.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/merge/test_template_coordinate.2.sam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/ZUKKp2UiXy/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/ZUKKp2UiXy/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/ZUKKp2UiXy/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -N -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -m 10M -M -K10 -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/ZUKKp2UiXy/sortout
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/ZUKKp2UiXy/sortout.bam
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam /tmp/ZUKKp2UiXy/sorttmp
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -N -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sort_name_input_1.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 --template-coordinate -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -m 10M -M -K10 -I /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/auto_indexed.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -@ 2 -m 10M -MH -K10 -I /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate1.tmp.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate2.tmp.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate2.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate3.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate1.tmp.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate2.tmp.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate2.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/collate3.tmp
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ok+.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ok-.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_draft.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_not_updated.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_not_updated_noML.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_bad_MN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_MN_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ML_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_noseq.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_bounds.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ok+.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ok-.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_draft.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_not_updated.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_not_updated_noML.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_not_updated_noMN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_bad_MN.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_MN_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ML_only.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_ML_wrong_len.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_noseq.sam -
.. ok

test_fixmate:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -@ 2 -M -z off -O sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/fixmate/mod_bounds.sam -
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools calmd -uAr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.ref.fa
.. ok

/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.ref.fa
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.cram
.. ok

test_idxstat:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools idxstats /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.sam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck -v  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_quickcheck:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v21.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader --in-place /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v30.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/addrprg/1_fixup.sam
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov -j /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools bedcov -c /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/bedcov/bedcov.bam
.. ok

.. ok

.. ok

.. ok

.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort  -t nn /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam |
                /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - 
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -p 5 -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%#.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d RG -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d an -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -d an -M 3 -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam  /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam
.. ok

test_split:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort  -@ 2 -t nn /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split_d_nn.sam |
                /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools split  -@ 2 --output-fmt sam -f /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/split/split.tmp.d_nn.0unk.sam - 
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG /tmp/ZUKKp2UiXy/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG /tmp/ZUKKp2UiXy/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/test.bed /tmp/ZUKKp2UiXy/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref_name.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref2.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools depth /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools depth -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/large_pos/longref.sam
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/ZUKKp2UiXy/longref.sam.gz
.. ok

test_large_positions:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort    -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
                     /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools fixmate -O sam --no-PG - - |
                     /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools sort    -O sam --no-PG -m 10M
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/primer_counts.tsv -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test2.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_reset:
	cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset --dupflag | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag < /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools view
.. ok

test_reset:
	cat /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam | /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.bam
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/test_input_1_a.cram
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam -e"@PG	ID:samtools	PN:samtools" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG sam_to_fixed_bam /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam -e"@PG	ID:" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index --no-PG /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam; grep /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output.tmp.sam -e"@PG"
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag --reject-PG bwa_index /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset  --dupflag /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_reset:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools reset /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/seq.sam -o /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/reset/output
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -qv /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -qv -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -qv /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -qv -a /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_checksum:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools checksum -@ 2 -m /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/'
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 2 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 2 -Q 8 -q 45 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 1 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam /tmp/ZUKKp2UiXy/sample1.sam
.. ok

test_coverage:
	/builddir/build/BUILD/samtools-1.23-build/samtools-1.23/samtools coverage --min-depth 4 /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/test/dat/sample.sam /tmp/ZUKKp2UiXy/sample1.sam
.. ok


Number of tests:
    total            .. 998
    passed           .. 966
    failed           .. 0
    expected failure .. 32
    unexpected pass  .. 0

test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg

=== Testing mpileup.reg regressions ===
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam

Expected   passes:   120
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="gawk" ../regression.sh depth.reg

=== Testing depth.reg regressions ===

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam

Expected   passes:   55
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="gawk" ../regression.sh cram-size.reg

=== Testing cram-size.reg regressions ===

Expected   passes:   5
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="gawk" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   77
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="gawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   77
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/cram_size && AWK="gawk" ../regression.sh cram_size.reg

=== Testing cram_size.reg regressions ===

Expected   passes:   3
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: samtools-1.23-1.fc44.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2DJ4bf
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ cd samtools-1.23
+ DOCDIR=/builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/AUTHORS /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/ChangeLog.old /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/NEWS.md /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/examples /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.zLWDW5
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ cd samtools-1.23
+ LICENSEDIR=/builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/licenses/samtools
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/licenses/samtools
+ cp -pr /builddir/build/BUILD/samtools-1.23-build/samtools-1.23/LICENSE /builddir/build/BUILD/samtools-1.23-build/BUILDROOT/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.23-1.fc44 samtools(x86-64) = 1.23-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl 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_ABI_DT_RELR)(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_1.11)(64bit) libhts.so.3(HTSLIB_1.12)(64bit) libhts.so.3(HTSLIB_1.14)(64bit) libhts.so.3(HTSLIB_1.15)(64bit) libhts.so.3(HTSLIB_1.16)(64bit) libhts.so.3(HTSLIB_1.17)(64bit) libhts.so.3(HTSLIB_1.18)(64bit) libhts.so.3(HTSLIB_1.2.1)(64bit) libhts.so.3(HTSLIB_1.21)(64bit) libhts.so.3(HTSLIB_1.22)(64bit) libhts.so.3(HTSLIB_1.23)(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) libhts.so.3(HTSLIB_1.9)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.23-1.fc44.x86_64
Provides: samtools-debugsource = 1.23-1.fc44 samtools-debugsource(x86-64) = 1.23-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-1.23-1.fc44.x86_64
Provides: debuginfo(build-id) = 030d0b93c100e6a22acb553d477c0702ef748990 debuginfo(build-id) = 11edf1be27b481327c4a612787a277ed2818ee47 debuginfo(build-id) = 1753f330d8d509a05b03a4ca09bf827572544ec3 debuginfo(build-id) = 2be634f058599f48a141545d80afdf3d66820565 debuginfo(build-id) = 33fde0f8ae6218f580ba602c46ff1cb9294d8d7f debuginfo(build-id) = 7af33f4ae62300f431013bc534bc50352a8d2010 debuginfo(build-id) = e727af49d485f7f655f569bbddcf9ee36e1d6d7e samtools-debuginfo = 1.23-1.fc44 samtools-debuginfo(x86-64) = 1.23-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(x86-64) = 1.23-1.fc44
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/samtools-1.23-build/BUILDROOT
Wrote: /builddir/build/RPMS/samtools-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.23-1.fc44.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.EKniKq
+ umask 022
+ cd /builddir/build/BUILD/samtools-1.23-build
+ test -d /builddir/build/BUILD/samtools-1.23-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/samtools-1.23-build
+ rm -rf /builddir/build/BUILD/samtools-1.23-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild samtools-1.23-1.fc44.src.rpm
Finish: build phase for samtools-1.23-1.fc44.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1769501806.001017/root/var/log/dnf5.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/samtools-1.23-1.fc44.src.rpm) Config(child) 0 minutes 57 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": "samtools-debugsource",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "src"
        },
        {
            "name": "samtools-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "samtools",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished