Warning: Permanently added '54.242.181.83' (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/10066099-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 1.6
PID: 9261
Logging PID: 9263
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 10066099,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '83436232d36d75a3868c654aad8cc10b0bc7e683',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'htslib',
 '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': '10066099-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/htslib /var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/bioinformatics/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib'...

Running: git checkout 83436232d36d75a3868c654aad8cc10b0bc7e683 --

cmd: ['git', 'checkout', '83436232d36d75a3868c654aad8cc10b0bc7e683', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib
rc: 0
stdout: 
stderr: Note: switching to '83436232d36d75a3868c654aad8cc10b0bc7e683'.

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 8343623 automatic import of htslib

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib
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 htslib-1.23.tar.bz2
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o htslib-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/htslib/htslib-1.23.tar.bz2/md5/686ccffe2ba88ec57d85cca0e3eb2f3a/htslib-1.23.tar.bz2
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 4786k  100 4786k    0     0  80.3M      0 --:--:-- --:--:-- --:--:-- 80.5M
INFO: Reading stdout from command: md5sum htslib-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-07pst4t6/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500767.470292 -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-07pst4t6/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-07pst4t6/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769500767.470292 -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-07pst4t6/htslib/htslib.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-1769500767.470292/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-971e9293-3690-4437-b2c9-3cc976c70e72
INFO: Checking that b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 image matches host's architecture
INFO: Copy content of container b78a5ab595ef3bb460c58c0d4addb3548a499318fd5430f2bd41793ef7781499 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1769500767.470292/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-971e9293-3690-4437-b2c9-3cc976c70e72
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_64-1769500767.470292/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% |   5.5 KiB/s |   1.6 KiB |  00m00s
 fedora                                 100% |  31.6 MiB/s |  22.0 MiB |  00m01s
>>> Downloading successful, but checksum doesn't match. Calculated: 6a1ebfd74b64d3c19669fd2cc961f2f3805c17bc613aae16afc72106f73b631f82570087b0ecebda3f10f4416e151ae8617b905e9fed41d6cd370d1b07fa93ae(sha512) 6a1ebfd74b64d3c19669fd2cc961f2f3805c17bc613aae16afc72106f73b631f82570087b0ecebda3f10f4416e151ae8617b905e9fed41d6cd370d1b07fa93ae(sha512) 6a1ebfd74b64d3c19669fd2cc961f2f3805c17bc613aae16afc72106f73b631f82570087b0ecebda3f10f4416e151ae8617b905e9fed41d6cd370d1b07fa93ae(sha512)  Expected: cf4f6f0708649b70abb5c1998349f597d71e4a7b1eee1f7d1c8b5f50d18acce7f72d142ec4bff6864bfba741f9c84e4f61a59132a6fac075813b00330a5cbaa5(sha512) 16f6bef710c8c235bc4f22de8af5cc8e33fe8e788ca6d8061dbe1a89324ecca10389f4e917cc179b941522ac38e77217188fc530a5194b4f09c5249c93a40f35(sha512) cb796b0e9894777d557107c03175db4a486ad36b3f77136fb26ee477859f5efc14db25472f6580d183d09581828de03283459d87023288d8a90399fdc7220a70(sha512)  - https://d2lzkl7pfhq30w.cloudfront.net/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/repomd.xml
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% |   4.6 MiB/s |  52.1 KiB |  00m00s
[  2/182] coreutils-0:9.9-4.fc44.x86_64 100% |  58.1 MiB/s |   1.2 MiB |  00m00s
[  3/182] cpio-0:2.15-6.fc43.x86_64     100% |  22.0 MiB/s | 293.1 KiB |  00m00s
[  4/182] bash-0:5.3.9-3.fc44.x86_64    100% |  67.6 MiB/s |   1.9 MiB |  00m00s
[  5/182] diffutils-0:3.12-5.fc44.x86_6 100% |  48.3 MiB/s | 395.3 KiB |  00m00s
[  6/182] fedora-release-common-0:44-0. 100% |   8.0 MiB/s |  24.7 KiB |  00m00s
[  7/182] findutils-1:4.10.0-7.fc44.x86 100% | 179.8 MiB/s | 552.5 KiB |  00m00s
[  8/182] glibc-minimal-langpack-0:2.42 100% |  18.8 MiB/s |  76.9 KiB |  00m00s
[  9/182] grep-0:3.12-3.fc44.x86_64     100% |  73.6 MiB/s | 301.6 KiB |  00m00s
[ 10/182] gzip-0:1.14-2.fc44.x86_64     100% |  58.3 MiB/s | 179.1 KiB |  00m00s
[ 11/182] patch-0:2.8-4.fc44.x86_64     100% |  37.5 MiB/s | 115.2 KiB |  00m00s
[ 12/182] info-0:7.2-7.fc44.x86_64      100% |  44.7 MiB/s | 182.9 KiB |  00m00s
[ 13/182] redhat-rpm-config-0:343-19.fc 100% |  25.9 MiB/s |  79.4 KiB |  00m00s
[ 14/182] rpm-build-0:6.0.1-2.fc44.x86_ 100% |  45.5 MiB/s | 139.9 KiB |  00m00s
[ 15/182] sed-0:4.9-7.fc44.x86_64       100% | 103.9 MiB/s | 319.2 KiB |  00m00s
[ 16/182] shadow-utils-2:4.18.0-7.fc44. 100% | 182.9 MiB/s |   1.3 MiB |  00m00s
[ 17/182] unzip-0:6.0-69.fc44.x86_64    100% |  39.0 MiB/s | 199.6 KiB |  00m00s
[ 18/182] tar-2:1.35-8.fc44.x86_64      100% | 121.1 MiB/s | 868.2 KiB |  00m00s
[ 19/182] which-0:2.23-4.fc44.x86_64    100% |  20.6 MiB/s |  42.2 KiB |  00m00s
[ 20/182] xz-1:5.8.2-2.fc44.x86_64      100% | 148.3 MiB/s | 607.2 KiB |  00m00s
[ 21/182] util-linux-0:2.41.3-12.fc44.x 100% | 150.6 MiB/s |   1.2 MiB |  00m00s
[ 22/182] gawk-0:5.3.2-3.fc44.x86_64    100% | 103.2 MiB/s |   1.1 MiB |  00m00s
[ 23/182] filesystem-0:3.18-52.fc44.x86 100% | 133.4 MiB/s |   1.3 MiB |  00m00s
[ 24/182] glibc-0:2.42.9000-25.fc44.x86 100% | 296.0 MiB/s |   2.4 MiB |  00m00s
[ 25/182] ncurses-libs-0:6.5-9.20250614 100% |  47.9 MiB/s | 343.1 KiB |  00m00s
[ 26/182] bzip2-libs-0:1.0.8-23.fc44.x8 100% |   8.6 MiB/s |  43.8 KiB |  00m00s
[ 27/182] libacl-0:2.3.2-6.fc44.x86_64  100% |   6.1 MiB/s |  24.8 KiB |  00m00s
[ 28/182] gmp-1:6.3.0-5.fc44.x86_64     100% |  63.0 MiB/s | 322.5 KiB |  00m00s
[ 29/182] coreutils-common-0:9.9-4.fc44 100% | 210.4 MiB/s |   2.1 MiB |  00m00s
[ 30/182] libcap-0:2.77-2.fc44.x86_64   100% |  14.4 MiB/s |  88.5 KiB |  00m00s
[ 31/182] libattr-0:2.5.2-8.fc44.x86_64 100% |   2.5 MiB/s |  17.9 KiB |  00m00s
[ 32/182] libselinux-0:3.9-7.fc44.x86_6 100% |  19.8 MiB/s | 101.6 KiB |  00m00s
[ 33/182] systemd-libs-0:259-9.fc44.x86 100% | 120.7 MiB/s | 865.2 KiB |  00m00s
[ 34/182] fedora-repos-0:44-0.1.noarch  100% |   1.8 MiB/s |   9.1 KiB |  00m00s
[ 35/182] glibc-common-0:2.42.9000-25.f 100% |  36.0 MiB/s | 368.9 KiB |  00m00s
[ 36/182] openssl-libs-1:3.5.4-2.fc44.x 100% | 130.6 MiB/s |   2.7 MiB |  00m00s
[ 37/182] pcre2-0:10.47-1.fc44.1.x86_64 100% |  22.6 MiB/s | 277.7 KiB |  00m00s
[ 38/182] ed-0:1.22.4-2.fc44.x86_64     100% |  13.9 MiB/s |  85.6 KiB |  00m00s
[ 39/182] R-srpm-macros-0:1.3.4-3.fc44. 100% |   3.5 MiB/s |  10.8 KiB |  00m00s
[ 40/182] ansible-srpm-macros-0:1-20.1. 100% |   6.5 MiB/s |  20.1 KiB |  00m00s
[ 41/182] cmake-srpm-macros-0:3.31.10-5 100% |   5.2 MiB/s |  10.6 KiB |  00m00s
[ 42/182] dwz-0:0.16-3.fc44.x86_64      100% |  45.2 MiB/s | 138.9 KiB |  00m00s
[ 43/182] build-reproducibility-srpm-ma 100% |   3.2 MiB/s |  13.0 KiB |  00m00s
[ 44/182] efi-srpm-macros-0:6-6.fc44.no 100% |   7.3 MiB/s |  22.6 KiB |  00m00s
[ 45/182] filesystem-srpm-macros-0:3.18 100% |   8.7 MiB/s |  26.6 KiB |  00m00s
[ 46/182] file-0:5.46-9.fc44.x86_64     100% |  16.0 MiB/s |  49.0 KiB |  00m00s
[ 47/182] fonts-srpm-macros-1:5.0.0-2.f 100% |  13.4 MiB/s |  27.4 KiB |  00m00s
[ 48/182] forge-srpm-macros-0:0.4.0-4.f 100% |   9.8 MiB/s |  20.0 KiB |  00m00s
[ 49/182] fpc-srpm-macros-0:1.3-16.fc44 100% |   3.9 MiB/s |   7.9 KiB |  00m00s
[ 50/182] gap-srpm-macros-0:2-2.fc44.no 100% |   4.5 MiB/s |   9.1 KiB |  00m00s
[ 51/182] ghc-srpm-macros-0:1.9.2-4.fc4 100% |   4.3 MiB/s |   8.9 KiB |  00m00s
[ 52/182] gnat-srpm-macros-0:7-2.fc44.n 100% |   4.3 MiB/s |   8.7 KiB |  00m00s
[ 53/182] go-srpm-macros-0:3.8.0-2.fc44 100% |  13.8 MiB/s |  28.2 KiB |  00m00s
[ 54/182] java-srpm-macros-0:1-8.fc44.n 100% |   4.0 MiB/s |   8.1 KiB |  00m00s
[ 55/182] kernel-srpm-macros-0:1.0-28.f 100% |   2.9 MiB/s |   9.0 KiB |  00m00s
[ 56/182] lua-srpm-macros-0:1-17.fc44.n 100% |   4.3 MiB/s |   8.9 KiB |  00m00s
[ 57/182] ocaml-srpm-macros-0:11-3.fc44 100% |   4.5 MiB/s |   9.3 KiB |  00m00s
[ 58/182] openblas-srpm-macros-0:2-21.f 100% |   3.8 MiB/s |   7.8 KiB |  00m00s
[ 59/182] package-notes-srpm-macros-0:0 100% |   4.5 MiB/s |   9.2 KiB |  00m00s
[ 60/182] perl-srpm-macros-0:1-61.fc44. 100% |   4.1 MiB/s |   8.4 KiB |  00m00s
[ 61/182] pyproject-srpm-macros-0:1.18. 100% |   4.4 MiB/s |  13.5 KiB |  00m00s
[ 62/182] python-srpm-macros-0:3.14-10. 100% |   7.8 MiB/s |  24.0 KiB |  00m00s
[ 63/182] qt5-srpm-macros-0:5.15.18-2.f 100% |   4.2 MiB/s |   8.7 KiB |  00m00s
[ 64/182] qt6-srpm-macros-0:6.10.1-2.fc 100% |   4.5 MiB/s |   9.2 KiB |  00m00s
[ 65/182] rust-srpm-macros-0:28.4-3.fc4 100% |   5.4 MiB/s |  11.1 KiB |  00m00s
[ 66/182] rpm-0:6.0.1-2.fc44.x86_64     100% | 188.2 MiB/s | 578.3 KiB |  00m00s
[ 67/182] tree-sitter-srpm-macros-0:0.4 100% |   6.6 MiB/s |  13.5 KiB |  00m00s
[ 68/182] zig-srpm-macros-0:1-8.fc44.no 100% |   4.3 MiB/s |   8.8 KiB |  00m00s
[ 69/182] zip-0:3.0-45.fc44.x86_64      100% |  86.1 MiB/s | 264.4 KiB |  00m00s
[ 70/182] debugedit-0:5.2-6.fc44.x86_64 100% |  42.3 MiB/s |  86.7 KiB |  00m00s
[ 71/182] elfutils-0:0.194-3.fc44.x86_6 100% | 190.1 MiB/s | 583.9 KiB |  00m00s
[ 72/182] elfutils-libelf-0:0.194-3.fc4 100% | 100.2 MiB/s | 205.1 KiB |  00m00s
[ 73/182] libarchive-0:3.8.4-2.fc44.x86 100% | 143.7 MiB/s | 441.4 KiB |  00m00s
[ 74/182] libgcc-0:16.0.1-0.3.fc44.1.x8 100% |  56.3 MiB/s | 115.4 KiB |  00m00s
[ 75/182] libstdc++-0:16.0.1-0.3.fc44.1 100% | 229.0 MiB/s | 937.9 KiB |  00m00s
[ 76/182] readline-0:8.3-4.fc44.x86_64  100% | 112.2 MiB/s | 229.8 KiB |  00m00s
[ 77/182] popt-0:1.19-10.fc44.x86_64    100% |  16.3 MiB/s |  66.9 KiB |  00m00s
[ 78/182] rpm-build-libs-0:6.0.1-2.fc44 100% |  43.0 MiB/s | 132.2 KiB |  00m00s
[ 79/182] rpm-libs-0:6.0.1-2.fc44.x86_6 100% | 135.2 MiB/s | 415.5 KiB |  00m00s
[ 80/182] zstd-0:1.5.7-5.fc44.x86_64    100% |  37.6 MiB/s | 192.5 KiB |  00m00s
[ 81/182] audit-libs-0:4.1.2-4.fc44.x86 100% |  23.0 MiB/s | 141.3 KiB |  00m00s
[ 82/182] libeconf-0:0.7.9-3.fc44.x86_6 100% |   7.1 MiB/s |  36.2 KiB |  00m00s
[ 83/182] libsemanage-0:3.9-5.fc44.x86_ 100% |  41.2 MiB/s | 126.6 KiB |  00m00s
[ 84/182] libxcrypt-0:4.5.2-3.fc44.x86_ 100% |  64.1 MiB/s | 131.2 KiB |  00m00s
[ 85/182] pam-libs-0:1.7.2-1.fc44.x86_6 100% |  19.2 MiB/s |  59.1 KiB |  00m00s
[ 86/182] setup-0:2.15.0-28.fc44.noarch 100% |  51.2 MiB/s | 157.2 KiB |  00m00s
[ 87/182] mpfr-0:4.2.2-3.fc44.x86_64    100% |  87.4 MiB/s | 357.8 KiB |  00m00s
[ 88/182] xz-libs-1:5.8.2-2.fc44.x86_64 100% |  22.8 MiB/s | 116.8 KiB |  00m00s
[ 89/182] libblkid-0:2.41.3-12.fc44.x86 100% |  25.3 MiB/s | 129.4 KiB |  00m00s
[ 90/182] libfdisk-0:2.41.3-12.fc44.x86 100% |  54.7 MiB/s | 168.1 KiB |  00m00s
[ 91/182] libcap-ng-0:0.9-5.fc44.x86_64 100% |  10.6 MiB/s |  32.7 KiB |  00m00s
[ 92/182] liblastlog2-0:2.41.3-12.fc44. 100% |  11.5 MiB/s |  23.5 KiB |  00m00s
[ 93/182] libmount-0:2.41.3-12.fc44.x86 100% |  41.7 MiB/s | 171.0 KiB |  00m00s
[ 94/182] libsmartcols-0:2.41.3-12.fc44 100% |  21.2 MiB/s |  86.9 KiB |  00m00s
[ 95/182] libuuid-0:2.41.3-12.fc44.x86_ 100% |   6.5 MiB/s |  26.6 KiB |  00m00s
[ 96/182] zlib-ng-compat-0:2.3.2-3.fc44 100% |  30.3 MiB/s |  93.0 KiB |  00m00s
[ 97/182] util-linux-core-0:2.41.3-12.f 100% | 108.9 MiB/s | 557.8 KiB |  00m00s
[ 98/182] glibc-gconv-extra-0:2.42.9000 100% | 180.1 MiB/s |   1.6 MiB |  00m00s
[ 99/182] ncurses-base-0:6.5-9.20250614 100% |  14.4 MiB/s |  88.2 KiB |  00m00s
[100/182] gnulib-l10n-0:20241231-2.fc44 100% |  24.5 MiB/s | 150.3 KiB |  00m00s
[101/182] libsepol-0:3.9-3.fc44.x86_64  100% | 118.1 MiB/s | 362.9 KiB |  00m00s
[102/182] ca-certificates-0:2025.2.80_v 100% | 158.4 MiB/s | 973.5 KiB |  00m00s
[103/182] crypto-policies-0:20251128-3. 100% |  16.0 MiB/s |  98.3 KiB |  00m00s
[104/182] fedora-gpg-keys-0:44-0.1.noar 100% |  27.1 MiB/s | 138.8 KiB |  00m00s
[105/182] fedora-repos-rawhide-0:44-0.1 100% |   4.2 MiB/s |   8.6 KiB |  00m00s
[106/182] pcre2-syntax-0:10.47-1.fc44.1 100% |  53.6 MiB/s | 164.7 KiB |  00m00s
[107/182] linkdupes-0:0.7.2-3.fc44.x86_ 100% | 115.6 MiB/s | 355.1 KiB |  00m00s
[108/182] add-determinism-0:0.7.2-3.fc4 100% | 122.9 MiB/s | 881.3 KiB |  00m00s
[109/182] file-libs-0:5.46-9.fc44.x86_6 100% | 119.1 MiB/s | 853.4 KiB |  00m00s
[110/182] curl-0:8.18.0-3.fc44.x86_64   100% |  47.1 MiB/s | 241.1 KiB |  00m00s
[111/182] elfutils-libs-0:0.194-3.fc44. 100% |  92.1 MiB/s | 282.8 KiB |  00m00s
[112/182] elfutils-debuginfod-client-0: 100% |  22.8 MiB/s |  46.7 KiB |  00m00s
[113/182] libzstd-0:1.5.7-5.fc44.x86_64 100% | 118.5 MiB/s | 364.2 KiB |  00m00s
[114/182] libxml2-0:2.12.10-6.fc44.x86_ 100% | 141.5 MiB/s | 724.6 KiB |  00m00s
[115/182] lz4-libs-0:1.10.0-4.fc44.x86_ 100% |  19.0 MiB/s |  77.7 KiB |  00m00s
[116/182] libgomp-0:16.0.1-0.3.fc44.1.x 100% |  91.4 MiB/s | 374.2 KiB |  00m00s
[117/182] rpm-sign-libs-0:6.0.1-2.fc44. 100% |  13.7 MiB/s |  28.0 KiB |  00m00s
[118/182] lua-libs-0:5.4.8-5.fc44.x86_6 100% |  44.5 MiB/s | 136.6 KiB |  00m00s
[119/182] rpm-sequoia-0:1.10.0-2.fc44.x 100% | 229.4 MiB/s | 939.7 KiB |  00m00s
[120/182] elfutils-default-yama-scope-0 100% |   3.9 MiB/s |  11.9 KiB |  00m00s
[121/182] sqlite-libs-0:3.51.2-1.fc44.x 100% | 156.1 MiB/s | 799.2 KiB |  00m00s
[122/182] json-c-0:0.18-8.fc44.x86_64   100% |  22.6 MiB/s |  46.3 KiB |  00m00s
[123/182] ima-evm-utils-libs-0:1.6.2-8. 100% |   9.8 MiB/s |  30.0 KiB |  00m00s
[124/182] gnupg2-0:2.4.9-4.fc44.x86_64  100% | 275.6 MiB/s |   1.7 MiB |  00m00s
[125/182] libfsverity-0:1.6-4.fc44.x86_ 100% |   3.8 MiB/s |  19.2 KiB |  00m00s
[126/182] gpgverify-0:2.2-4.fc44.noarch 100% |   5.5 MiB/s |  11.2 KiB |  00m00s
[127/182] gnupg2-gpg-agent-0:2.4.9-4.fc 100% |  91.6 MiB/s | 281.4 KiB |  00m00s
[128/182] gnupg2-gpgconf-0:2.4.9-4.fc44 100% |  28.6 MiB/s | 117.2 KiB |  00m00s
[129/182] gnupg2-dirmngr-0:2.4.9-4.fc44 100% |  55.2 MiB/s | 282.5 KiB |  00m00s
[130/182] gnupg2-keyboxd-0:2.4.9-4.fc44 100% |  47.6 MiB/s |  97.4 KiB |  00m00s
[131/182] gnupg2-verify-0:2.4.9-4.fc44. 100% |  57.6 MiB/s | 176.9 KiB |  00m00s
[132/182] libassuan-0:2.5.7-5.fc44.x86_ 100% |  22.4 MiB/s |  68.9 KiB |  00m00s
[133/182] libgcrypt-0:1.11.2-1.fc44.x86 100% |  97.0 MiB/s | 596.1 KiB |  00m00s
[134/182] libgpg-error-0:1.58-2.fc44.x8 100% |  49.6 MiB/s | 254.1 KiB |  00m00s
[135/182] npth-0:1.8-4.fc44.x86_64      100% |   5.0 MiB/s |  25.8 KiB |  00m00s
[136/182] tpm2-tss-0:4.1.3-9.fc44.x86_6 100% | 143.5 MiB/s | 440.9 KiB |  00m00s
[137/182] gnutls-0:3.8.11-10.fc44.x86_6 100% | 233.6 MiB/s |   1.4 MiB |  00m00s
[138/182] libksba-0:1.6.7-5.fc44.x86_64 100% |  23.3 MiB/s | 167.4 KiB |  00m00s
[139/182] openldap-0:2.6.10-7.fc44.x86_ 100% |  52.9 MiB/s | 271.1 KiB |  00m00s
[140/182] libusb1-0:1.0.29-5.fc44.x86_6 100% |  40.4 MiB/s |  82.8 KiB |  00m00s
[141/182] libidn2-0:2.3.8-3.fc44.x86_64 100% |  85.7 MiB/s | 175.6 KiB |  00m00s
[142/182] libtasn1-0:4.20.0-3.fc44.x86_ 100% |  37.2 MiB/s |  76.2 KiB |  00m00s
[143/182] nettle-0:3.10.1-3.fc44.x86_64 100% | 139.3 MiB/s | 428.0 KiB |  00m00s
[144/182] libunistring-0:1.1-11.fc44.x8 100% | 107.0 MiB/s | 547.8 KiB |  00m00s
[145/182] p11-kit-0:0.25.8-2.fc44.x86_6 100% | 126.1 MiB/s | 516.5 KiB |  00m00s
[146/182] cyrus-sasl-lib-0:2.1.28-35.fc 100% | 195.5 MiB/s | 800.7 KiB |  00m00s
[147/182] libevent-0:2.1.12-17.fc44.x86 100% |  70.2 MiB/s | 287.4 KiB |  00m00s
[148/182] libtool-ltdl-0:2.5.4-10.fc44. 100% |  12.1 MiB/s |  37.0 KiB |  00m00s
[149/182] libffi-0:3.5.2-2.fc44.x86_64  100% |  20.7 MiB/s |  42.4 KiB |  00m00s
[150/182] gdbm-libs-1:1.23-11.fc44.x86_ 100% |  28.7 MiB/s |  58.8 KiB |  00m00s
[151/182] alternatives-0:1.33-5.fc44.x8 100% |  13.3 MiB/s |  40.8 KiB |  00m00s
[152/182] pkgconf-pkg-config-0:2.3.0-4. 100% |   2.4 MiB/s |   9.7 KiB |  00m00s
[153/182] jansson-0:2.14-4.fc44.x86_64  100% |   7.7 MiB/s |  47.1 KiB |  00m00s
[154/182] pkgconf-0:2.3.0-4.fc44.x86_64 100% |  22.0 MiB/s |  45.0 KiB |  00m00s
[155/182] pkgconf-m4-0:2.3.0-4.fc44.noa 100% |   3.4 MiB/s |  14.1 KiB |  00m00s
[156/182] binutils-0:2.45.50-19.fc44.x8 100% | 289.7 MiB/s |   6.1 MiB |  00m00s
[157/182] libpkgconf-0:2.3.0-4.fc44.x86 100% |   4.2 MiB/s |  38.8 KiB |  00m00s
[158/182] p11-kit-trust-0:0.25.8-2.fc44 100% |  20.2 MiB/s | 144.8 KiB |  00m00s
[159/182] fedora-release-0:44-0.10.noar 100% |   3.3 MiB/s |  13.5 KiB |  00m00s
[160/182] systemd-standalone-sysusers-0 100% |  29.0 MiB/s | 148.3 KiB |  00m00s
[161/182] gdb-minimal-0:17.1-2.fc44.x86 100% | 251.9 MiB/s |   4.8 MiB |  00m00s
[162/182] fedora-release-identity-basic 100% | 951.8 KiB/s |  14.3 KiB |  00m00s
[163/182] xxhash-libs-0:0.8.3-4.fc44.x8 100% |   2.5 MiB/s |  41.2 KiB |  00m00s
[164/182] krb5-libs-0:1.21.3-12.fc44.x8 100% | 155.0 MiB/s | 793.5 KiB |  00m00s
[165/182] libbrotli-0:1.2.0-3.fc44.x86_ 100% |  67.9 MiB/s | 347.8 KiB |  00m00s
[166/182] libcurl-0:8.18.0-3.fc44.x86_6 100% |  74.1 MiB/s | 455.1 KiB |  00m00s
[167/182] libnghttp2-0:1.68.0-3.fc44.x8 100% |  37.7 MiB/s |  77.2 KiB |  00m00s
[168/182] libnghttp3-0:1.15.0-1.fc44.x8 100% |  36.1 MiB/s |  73.9 KiB |  00m00s
[169/182] libpsl-0:0.21.5-7.fc44.x86_64 100% |  31.9 MiB/s |  65.3 KiB |  00m00s
[170/182] libssh-0:0.11.3-1.fc44.x86_64 100% | 113.7 MiB/s | 232.8 KiB |  00m00s
[171/182] ngtcp2-0:1.19.0-2.fc44.x86_64 100% |  75.6 MiB/s | 154.8 KiB |  00m00s
[172/182] ngtcp2-crypto-ossl-0:1.19.0-2 100% |  13.4 MiB/s |  27.4 KiB |  00m00s
[173/182] keyutils-libs-0:1.6.3-7.fc44. 100% |  15.4 MiB/s |  31.5 KiB |  00m00s
[174/182] libcom_err-0:1.47.3-4.fc44.x8 100% |  13.2 MiB/s |  27.1 KiB |  00m00s
[175/182] libverto-0:0.3.2-12.fc44.x86_ 100% |  10.3 MiB/s |  21.1 KiB |  00m00s
[176/182] publicsuffix-list-dafsa-0:202 100% |  29.4 MiB/s |  60.3 KiB |  00m00s
[177/182] libssh-config-0:0.11.3-1.fc44 100% |   4.4 MiB/s |   9.1 KiB |  00m00s
[178/182] selinux-policy-0:42.22-1.fc44 100% |   6.6 MiB/s |  67.8 KiB |  00m00s
[179/182] policycoreutils-0:3.9-8.fc44. 100% |  23.0 MiB/s | 258.6 KiB |  00m00s
[180/182] selinux-policy-targeted-0:42. 100% | 309.6 MiB/s |   6.8 MiB |  00m00s
[181/182] libselinux-utils-0:3.9-7.fc44 100% |  11.7 MiB/s | 119.7 KiB |  00m00s
[182/182] rpm-plugin-selinux-0:6.0.1-2. 100% |   2.1 MiB/s |  19.2 KiB |  00m00s
--------------------------------------------------------------------------------
[182/182] Total                         100% | 202.0 MiB/s |  68.5 MiB |  00m00s
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% | 761.0   B/s | 182.0   B |  00m00s
[  2/184] Prepare transaction           100% |   3.8 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% |  58.3 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% |   3.1 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% | 431.9 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% | 302.9 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% | 204.4 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% |  79.7 MiB/s |  81.6 KiB |  00m00s
[ 27/184] Installing libgpg-error-0:1.5 100% |  71.2 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% | 467.5 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% | 407.0 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% |  20.5 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% |  71.6 MiB/s |   1.0 MiB |  00m00s
[ 50/184] Installing sed-0:4.9-7.fc44.x 100% |  65.0 MiB/s | 865.4 KiB |  00m00s
[ 51/184] Installing findutils-1:4.10.0 100% | 116.8 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% | 433.6 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% |  80.5 MiB/s |   1.4 MiB |  00m00s
[ 57/184] Installing libmount-0:2.41.3- 100% | 380.6 MiB/s | 389.7 KiB |  00m00s
[ 58/184] Installing gnupg2-verify-0:2. 100% |  29.4 MiB/s | 361.7 KiB |  00m00s
[ 59/184] Installing dwz-0:0.16-3.fc44. 100% |  25.9 MiB/s | 292.3 KiB |  00m00s
[ 60/184] Installing mpfr-0:4.2.2-3.fc4 100% | 415.4 MiB/s | 850.8 KiB |  00m00s
[ 61/184] Installing gawk-0:5.3.2-3.fc4 100% | 114.6 MiB/s |   1.8 MiB |  00m00s
[ 62/184] Installing libksba-0:1.6.7-5. 100% | 407.1 MiB/s | 416.9 KiB |  00m00s
[ 63/184] Installing unzip-0:6.0-69.fc4 100% |  36.6 MiB/s | 449.3 KiB |  00m00s
[ 64/184] Installing file-libs-0:5.46-9 100% | 741.3 MiB/s |  11.9 MiB |  00m00s
[ 65/184] Installing file-0:5.46-9.fc44 100% |   9.0 MiB/s | 101.6 KiB |  00m00s
[ 66/184] Installing diffutils-0:3.12-5 100% | 104.8 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% |   0.0   B/s |  70.5 KiB |  00m00s
[ 69/184] Installing audit-libs-0:4.1.2 100% | 383.7 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% |  17.7 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% |   0.0   B/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% | 128.7 MiB/s |   2.3 MiB |  00m00s
[ 78/184] Installing alternatives-0:1.3 100% |   5.6 MiB/s |  63.6 KiB |  00m00s
[ 79/184] Installing p11-kit-trust-0:0. 100% |  25.0 MiB/s | 460.0 KiB |  00m00s
[ 80/184] Installing ngtcp2-0:1.19.0-2. 100% | 323.9 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% | 177.0 MiB/s |   5.5 MiB |  00m00s
[ 83/184] Installing ca-certificates-0: 100% |   2.3 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% |  92.7 MiB/s |   1.5 MiB |  00m00s
[ 90/184] Installing zip-0:3.0-45.fc44. 100% |  57.1 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% | 156.7 MiB/s |   3.0 MiB |  00m00s
[ 94/184] Installing linkdupes-0:0.7.2- 100% |  62.2 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% |  24.6 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% | 326.6 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% |  35.3 MiB/s | 686.5 KiB |  00m00s
[103/184] Installing libfdisk-0:2.41.3- 100% | 190.2 MiB/s | 389.4 KiB |  00m00s
[104/184] Installing util-linux-0:2.41. 100% | 108.6 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% | 205.6 MiB/s |  14.8 MiB |  00m00s
[108/184] Installing zstd-0:1.5.7-5.fc4 100% |  32.9 MiB/s | 506.0 KiB |  00m00s
[109/184] Installing libxml2-0:2.12.10- 100% | 118.0 MiB/s |   1.8 MiB |  00m00s
[110/184] Installing nettle-0:3.10.1-3. 100% | 389.4 MiB/s | 797.4 KiB |  00m00s
[111/184] Installing gnutls-0:3.8.11-10 100% | 414.5 MiB/s |   3.7 MiB |  00m00s
[112/184] Installing bzip2-0:1.0.8-23.f 100% |   8.8 MiB/s |  99.5 KiB |  00m00s
[113/184] Installing add-determinism-0: 100% | 141.8 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% |  20.2 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% | 559.5 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% | 144.4 MiB/s |   2.3 MiB |  00m00s
[124/184] Installing openldap-0:2.6.10- 100% | 327.8 MiB/s | 671.3 KiB |  00m00s
[125/184] Installing gnupg2-dirmngr-0:2 100% |  34.5 MiB/s | 636.7 KiB |  00m00s
[126/184] Installing gnupg2-0:2.4.9-4.f 100% | 241.0 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% |   8.1 MiB/s |  90.8 KiB |  00m00s
[132/184] Installing pkgconf-pkg-config 100% | 177.3 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% |   0.0   B/s |  55.6 KiB |  00m00s
[138/184] Installing libcom_err-0:1.47. 100% |   0.0   B/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% |  23.6 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% |  40.2 MiB/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% |   6.5 MiB/s |  86.0 KiB |  00m00s
[155/184] Installing elfutils-0:0.194-3 100% | 164.4 MiB/s |   3.0 MiB |  00m00s
[156/184] Installing binutils-0:2.45.50 100% | 352.3 MiB/s |  27.5 MiB |  00m00s
[157/184] Installing gdb-minimal-0:17.1 100% | 304.9 MiB/s |  14.3 MiB |  00m00s
[158/184] Installing debugedit-0:5.2-6. 100% |  18.0 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% | 185.4 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% |  22.8 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% | 152.8 MiB/s |   4.0 MiB |  00m00s
[184/184] Installing info-0:7.2-7.fc44. 100% |  52.7 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/htslib-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_64-1769500767.470292/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-07pst4t6/htslib/htslib.spec) Config(child) 0 minutes 21 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/htslib-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-1769500767.470292/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1769500767.470292/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_64-1769500767.470292/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 htslib-1.23-1.fc44.src.rpm
Start: build setup for htslib-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/htslib-1.23-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% | 107.8 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 239.9 KiB/s |  26.4 KiB |  00m00s
Repositories loaded.
Package                   Arch   Version                Repository      Size
Installing:
 bzip2-devel              x86_64 0:1.0.8-23.fc44        fedora     309.8 KiB
 gcc                      x86_64 0:16.0.1-0.3.fc44.1    fedora     120.6 MiB
 libcurl-devel            x86_64 0:8.18.0-3.fc44        fedora       1.4 MiB
 make                     x86_64 1:4.4.1-12.fc44        fedora       1.8 MiB
 openssl-devel            x86_64 1:3.5.4-2.fc44         fedora       4.6 MiB
 perl-Data-Dumper         x86_64 0:2.191-522.fc44       fedora     115.5 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
 xz-devel                 x86_64 1:5.8.2-2.fc44         fedora     258.8 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
 brotli                   x86_64 0:1.2.0-3.fc44         fedora      33.4 KiB
 brotli-devel             x86_64 0:1.2.0-3.fc44         fedora      65.9 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
 kernel-headers           x86_64 0:6.19.0-0.rc6.43.fc44 fedora       6.9 MiB
 keyutils-libs-devel      x86_64 0:1.6.3-7.fc44         fedora      48.2 KiB
 krb5-devel               x86_64 0:1.21.3-12.fc44       fedora     705.9 KiB
 libatomic                x86_64 0:16.0.1-0.3.fc44.1    fedora      45.3 KiB
 libcom_err-devel         x86_64 0:1.47.3-4.fc44        fedora      16.7 KiB
 libidn2-devel            x86_64 0:2.3.8-3.fc44         fedora     149.1 KiB
 libkadm5                 x86_64 0:1.21.3-12.fc44       fedora     217.8 KiB
 libmpc                   x86_64 0:1.3.1-9.fc44         fedora     160.4 KiB
 libnghttp2-devel         x86_64 0:1.68.0-3.fc44        fedora     288.0 KiB
 libnghttp3-devel         x86_64 0:1.15.0-1.fc44        fedora     107.4 KiB
 libpsl-devel             x86_64 0:0.21.5-7.fc44        fedora     110.2 KiB
 libselinux-devel         x86_64 0:3.9-7.fc44           fedora     121.6 KiB
 libsepol-devel           x86_64 0:3.9-3.fc44           fedora     121.4 KiB
 libssh-devel             x86_64 0:0.11.3-1.fc44        fedora     178.0 KiB
 libverto-devel           x86_64 0:0.3.2-12.fc44        fedora      25.7 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
 ngtcp2-crypto-ossl-devel x86_64 0:1.19.0-2.fc44        fedora       7.5 KiB
 ngtcp2-devel             x86_64 0:1.19.0-2.fc44        fedora     282.4 KiB
 pcre2-devel              x86_64 0:10.47-1.fc44.1       fedora       2.1 MiB
 pcre2-utf16              x86_64 0:10.47-1.fc44.1       fedora     655.2 KiB
 pcre2-utf32              x86_64 0:10.47-1.fc44.1       fedora     623.1 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-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
 publicsuffix-list        noarch 0:20260116-1.fc44      fedora     342.2 KiB

Transaction Summary:
 Installing:        99 packages

Total size of inbound packages is 76 MiB. Need to download 76 MiB.
After this operation, 215 MiB extra will be used (install 215 MiB, remove 0 B).
[ 1/99] perl-Data-Dumper-0:2.191-522.fc 100% |   3.7 MiB/s |  56.5 KiB |  00m00s
[ 2/99] perl-FindBin-0:1.54-521.fc44.no 100% |   2.7 MiB/s |  13.9 KiB |  00m00s
[ 3/99] make-1:4.4.1-12.fc44.x86_64     100% |  25.0 MiB/s | 588.7 KiB |  00m00s
[ 4/99] perl-Getopt-Long-1:2.58-521.fc4 100% |   8.9 MiB/s |  63.6 KiB |  00m00s
[ 5/99] perl-lib-0:0.65-521.fc44.x86_64 100% |   2.0 MiB/s |  14.6 KiB |  00m00s
[ 6/99] perl-interpreter-4:5.42.0-521.f 100% |   8.8 MiB/s |  72.0 KiB |  00m00s
[ 7/99] bzip2-devel-0:1.0.8-23.fc44.x86 100% |  23.2 MiB/s | 213.7 KiB |  00m00s
[ 8/99] libcurl-devel-0:8.18.0-3.fc44.x 100% |  50.9 MiB/s | 938.0 KiB |  00m00s
[ 9/99] xz-devel-1:5.8.2-2.fc44.x86_64  100% |   9.3 MiB/s |  67.0 KiB |  00m00s
[10/99] zlib-ng-compat-devel-0:2.3.2-3. 100% |   3.7 MiB/s |  38.0 KiB |  00m00s
[11/99] cpp-0:16.0.1-0.3.fc44.1.x86_64  100% | 190.1 MiB/s |  14.4 MiB |  00m00s
[12/99] libmpc-0:1.3.1-9.fc44.x86_64    100% |  17.6 MiB/s |  72.1 KiB |  00m00s
[13/99] gcc-0:16.0.1-0.3.fc44.1.x86_64  100% | 224.9 MiB/s |  43.0 MiB |  00m00s
[14/99] perl-B-0:1.89-521.fc44.x86_64   100% |   4.7 MiB/s | 177.6 KiB |  00m00s
[15/99] openssl-devel-1:3.5.4-2.fc44.x8 100% |  19.2 MiB/s |   3.0 MiB |  00m00s
[16/99] perl-Carp-0:1.54-521.fc44.noarc 100% |   4.7 MiB/s |  28.8 KiB |  00m00s
[17/99] perl-Exporter-0:5.79-521.fc44.n 100% |   6.0 MiB/s |  30.8 KiB |  00m00s
[18/99] perl-Scalar-List-Utils-5:1.70-2 100% |  36.8 MiB/s |  75.4 KiB |  00m00s
[19/99] perl-constant-0:1.33-522.fc44.n 100% |  11.2 MiB/s |  22.9 KiB |  00m00s
[20/99] perl-libs-4:5.42.0-521.fc44.x86 100% | 286.3 MiB/s |   2.6 MiB |  00m00s
[21/99] perl-File-Basename-0:2.86-521.f 100% |   2.3 MiB/s |  16.8 KiB |  00m00s
[22/99] perl-PathTools-0:3.94-521.fc44. 100% |  12.2 MiB/s |  87.3 KiB |  00m00s
[23/99] perl-Pod-Usage-4:2.05-521.fc44. 100% |  19.9 MiB/s |  40.7 KiB |  00m00s
[24/99] perl-Text-ParseWords-0:3.31-521 100% |   8.0 MiB/s |  16.5 KiB |  00m00s
[25/99] perl-base-0:2.27-521.fc44.noarc 100% |   7.8 MiB/s |  15.9 KiB |  00m00s
[26/99] perl-overload-0:1.40-521.fc44.n 100% |  44.1 MiB/s |  45.2 KiB |  00m00s
[27/99] perl-if-0:0.61.000-521.fc44.noa 100% |  13.3 MiB/s |  13.7 KiB |  00m00s
[28/99] perl-overloading-0:0.02-521.fc4 100% |   6.1 MiB/s |  12.6 KiB |  00m00s
[29/99] cmake-filesystem-0:3.31.10-5.fc 100% |   3.5 MiB/s |  14.1 KiB |  00m00s
[30/99] perl-DynaLoader-0:1.57-521.fc44 100% |  12.5 MiB/s |  25.7 KiB |  00m00s
[31/99] perl-Errno-0:1.38-521.fc44.x86_ 100% |   3.6 MiB/s |  14.6 KiB |  00m00s
[32/99] perl-Pod-Perldoc-0:3.28.01-522. 100% |  21.0 MiB/s |  86.1 KiB |  00m00s
[33/99] perl-podlators-1:6.0.2-521.fc44 100% |  31.4 MiB/s | 128.5 KiB |  00m00s
[34/99] perl-mro-0:1.29-521.fc44.x86_64 100% |  14.4 MiB/s |  29.5 KiB |  00m00s
[35/99] perl-vars-0:1.05-521.fc44.noarc 100% |   6.2 MiB/s |  12.6 KiB |  00m00s
[36/99] groff-base-0:1.23.0-12.fc44.x86 100% | 224.7 MiB/s |   1.1 MiB |  00m00s
[37/99] perl-Fcntl-0:1.20-521.fc44.x86_ 100% |   7.2 MiB/s |  29.3 KiB |  00m00s
[38/99] perl-File-Temp-1:0.231.200-2.fc 100% |  14.5 MiB/s |  59.6 KiB |  00m00s
[39/99] perl-HTTP-Tiny-0:0.092-2.fc44.n 100% |  27.9 MiB/s |  57.2 KiB |  00m00s
[40/99] perl-IO-0:1.55-521.fc44.x86_64  100% |  40.0 MiB/s |  81.8 KiB |  00m00s
[41/99] perl-IPC-Open3-0:1.24-521.fc44. 100% |  11.5 MiB/s |  23.6 KiB |  00m00s
[42/99] perl-Pod-Simple-1:3.47-4.fc44.n 100% | 107.4 MiB/s | 220.0 KiB |  00m00s
[43/99] perl-Symbol-0:1.09-521.fc44.noa 100% |   6.8 MiB/s |  13.9 KiB |  00m00s
[44/99] perl-parent-1:0.244-521.fc44.no 100% |   7.3 MiB/s |  14.9 KiB |  00m00s
[45/99] perl-POSIX-0:2.23-521.fc44.x86_ 100% |  47.7 MiB/s |  97.6 KiB |  00m00s
[46/99] perl-Term-ANSIColor-0:5.01-522. 100% |  15.5 MiB/s |  47.7 KiB |  00m00s
[47/99] perl-Term-Cap-0:1.18-521.fc44.n 100% |   7.2 MiB/s |  22.0 KiB |  00m00s
[48/99] perl-File-Path-0:2.18-522.fc44. 100% |  34.4 MiB/s |  35.3 KiB |  00m00s
[49/99] perl-IO-Socket-SSL-0:2.098-2.fc 100% |  76.4 MiB/s | 234.7 KiB |  00m00s
[50/99] perl-MIME-Base64-0:3.16-521.fc4 100% |   7.3 MiB/s |  29.8 KiB |  00m00s
[51/99] perl-Net-SSLeay-0:1.94-12.fc44. 100% |  72.9 MiB/s | 373.4 KiB |  00m00s
[52/99] perl-Socket-4:2.040-3.fc44.x86_ 100% |  18.0 MiB/s |  55.3 KiB |  00m00s
[53/99] perl-Time-HiRes-4:1.9778-521.fc 100% |  18.6 MiB/s |  57.2 KiB |  00m00s
[54/99] perl-Time-Local-2:1.350-521.fc4 100% |  33.7 MiB/s |  34.5 KiB |  00m00s
[55/99] perl-File-stat-0:1.14-521.fc44. 100% |  16.3 MiB/s |  16.7 KiB |  00m00s
[56/99] perl-SelectSaver-0:1.02-521.fc4 100% |   5.6 MiB/s |  11.4 KiB |  00m00s
[57/99] perl-Pod-Escapes-1:1.07-521.fc4 100% |  19.3 MiB/s |  19.8 KiB |  00m00s
[58/99] perl-Text-Tabs+Wrap-0:2024.001- 100% |  10.6 MiB/s |  21.8 KiB |  00m00s
[59/99] perl-locale-0:1.13-521.fc44.noa 100% |   6.4 MiB/s |  13.2 KiB |  00m00s
[60/99] ncurses-0:6.5-9.20250614.fc44.x 100% | 139.2 MiB/s | 427.6 KiB |  00m00s
[61/99] perl-IO-Socket-IP-0:0.43-522.fc 100% |  20.6 MiB/s |  42.2 KiB |  00m00s
[62/99] perl-URI-0:5.34-3.fc44.noarch   100% |  72.9 MiB/s | 149.2 KiB |  00m00s
[63/99] perl-AutoLoader-0:5.74-521.fc44 100% |  10.2 MiB/s |  20.9 KiB |  00m00s
[64/99] perl-Class-Struct-0:0.68-521.fc 100% |  10.6 MiB/s |  21.7 KiB |  00m00s
[65/99] perl-MIME-Base32-0:1.303-25.fc4 100% |  20.0 MiB/s |  20.5 KiB |  00m00s
[66/99] perl-libnet-0:3.15-522.fc44.noa 100% |  41.8 MiB/s | 128.4 KiB |  00m00s
[67/99] perl-Digest-MD5-0:2.59-521.fc44 100% |  11.7 MiB/s |  36.0 KiB |  00m00s
[68/99] perl-FileHandle-0:2.05-521.fc44 100% |   4.9 MiB/s |  15.2 KiB |  00m00s
[69/99] perl-Digest-0:1.20-521.fc44.noa 100% |  24.3 MiB/s |  24.9 KiB |  00m00s
[70/99] perl-Encode-4:3.21-521.fc44.x86 100% | 263.0 MiB/s |   1.1 MiB |  00m00s
[71/99] perl-Getopt-Std-0:1.14-521.fc44 100% |   5.0 MiB/s |  15.3 KiB |  00m00s
[72/99] perl-Storable-1:3.37-522.fc44.x 100% |  32.8 MiB/s | 100.9 KiB |  00m00s
[73/99] brotli-0:1.2.0-3.fc44.x86_64    100% |   7.9 MiB/s |  24.1 KiB |  00m00s
[74/99] krb5-devel-0:1.21.3-12.fc44.x86 100% |  46.3 MiB/s | 142.2 KiB |  00m00s
[75/99] brotli-devel-0:1.2.0-3.fc44.x86 100% |   5.6 MiB/s |  34.6 KiB |  00m00s
[76/99] libkadm5-0:1.21.3-12.fc44.x86_6 100% |  25.7 MiB/s |  79.0 KiB |  00m00s
[77/99] libidn2-devel-0:2.3.8-3.fc44.x8 100% |  20.9 MiB/s |  64.1 KiB |  00m00s
[78/99] libnghttp2-devel-0:1.68.0-3.fc4 100% |  13.3 MiB/s |  54.6 KiB |  00m00s
[79/99] libnghttp3-devel-0:1.15.0-1.fc4 100% |   6.4 MiB/s |  26.4 KiB |  00m00s
[80/99] libpsl-devel-0:0.21.5-7.fc44.x8 100% |   8.0 MiB/s |  32.8 KiB |  00m00s
[81/99] libssh-devel-0:0.11.3-1.fc44.x8 100% |  13.6 MiB/s |  41.8 KiB |  00m00s
[82/99] publicsuffix-list-0:20260116-1. 100% |  29.9 MiB/s |  91.7 KiB |  00m00s
[83/99] ngtcp2-crypto-ossl-devel-0:1.19 100% |   3.6 MiB/s |  11.0 KiB |  00m00s
[84/99] ngtcp2-devel-0:1.19.0-2.fc44.x8 100% |  17.2 MiB/s |  53.0 KiB |  00m00s
[85/99] keyutils-libs-devel-0:1.6.3-7.f 100% |  19.4 MiB/s |  59.7 KiB |  00m00s
[86/99] libcom_err-devel-0:1.47.3-4.fc4 100% |   5.5 MiB/s |  16.8 KiB |  00m00s
[87/99] libselinux-devel-0:3.9-7.fc44.x 100% |  49.4 MiB/s | 151.8 KiB |  00m00s
[88/99] libsepol-devel-0:3.9-3.fc44.x86 100% |  15.7 MiB/s |  48.2 KiB |  00m00s
[89/99] libverto-devel-0:0.3.2-12.fc44. 100% |   4.7 MiB/s |  14.4 KiB |  00m00s
[90/99] glibc-devel-0:2.42.9000-25.fc44 100% | 199.3 MiB/s | 612.1 KiB |  00m00s
[91/99] libxcrypt-devel-0:4.5.2-3.fc44. 100% |   9.8 MiB/s |  30.0 KiB |  00m00s
[92/99] libatomic-0:16.0.1-0.3.fc44.1.x 100% |  11.1 MiB/s |  34.0 KiB |  00m00s
[93/99] pcre2-devel-0:10.47-1.fc44.1.x8 100% | 179.3 MiB/s | 550.9 KiB |  00m00s
[94/99] pcre2-utf32-0:10.47-1.fc44.1.x8 100% |  39.4 MiB/s | 242.2 KiB |  00m00s
[95/99] kernel-headers-0:6.19.0-0.rc6.4 100% | 216.4 MiB/s |   1.7 MiB |  00m00s
[96/99] pcre2-utf16-0:10.47-1.fc44.1.x8 100% |  20.9 MiB/s | 256.3 KiB |  00m00s
[97/99] annobin-plugin-gcc-0:13.05-3.fc 100% | 111.2 MiB/s | 683.1 KiB |  00m00s
[98/99] gcc-plugin-annobin-0:16.0.1-0.3 100% |  18.5 MiB/s |  37.8 KiB |  00m00s
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--------------------------------------------------------------------------------
[99/99] Total                           100% | 250.9 MiB/s |  75.8 MiB |  00m00s
Running transaction
[  1/101] Verify package files          100% | 399.0   B/s |  99.0   B |  00m00s
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[  9/101] Installing zlib-ng-compat-dev 100% | 106.0 MiB/s | 108.6 KiB |  00m00s
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[ 27/101] Installing libnghttp2-devel-0 100% | 282.3 MiB/s | 289.1 KiB |  00m00s
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[ 29/101] Installing libkadm5-0:1.21.3- 100% | 214.6 MiB/s | 219.8 KiB |  00m00s
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[ 47/101] Installing perl-locale-0:1.13 100% |   0.0   B/s |   6.5 KiB |  00m00s
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Complete!
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/htslib-1.23-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |   2.5 KiB/s |   1.5 KiB |  00m01s
 fedora                                 100% |  35.7 KiB/s |  26.4 KiB |  00m01s
Repositories loaded.
Nothing to do.
Package "bzip2-devel-1.0.8-23.fc44.x86_64" is already installed.
Package "gcc-16.0.1-0.3.fc44.1.x86_64" is already installed.
Package "libcurl-devel-8.18.0-3.fc44.x86_64" is already installed.
Package "make-1:4.4.1-12.fc44.x86_64" is already installed.
Package "openssl-devel-1:3.5.4-2.fc44.x86_64" is already installed.
Package "perl-Data-Dumper-2.191-522.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 "xz-devel-1:5.8.2-2.fc44.x86_64" is already installed.
Package "zlib-ng-compat-devel-2.3.2-3.fc44.x86_64" is already installed.

Finish: build setup for htslib-1.23-1.fc44.src.rpm
Start: rpmbuild htslib-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.TGVp62
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.0H332a
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.23-build
+ cd /builddir/build/BUILD/htslib-1.23-build
+ rm -rf htslib-1.23
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.23.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd htslib-1.23
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.j94AxN
+ umask 022
+ cd /builddir/build/BUILD/htslib-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 htslib-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' ./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 ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
++ basename ./config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3
configure: WARNING: unrecognized options: --disable-dependency-tracking
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 x86_64-redhat-linux-ranlib... no
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for gcc options needed to detect all undeclared functions... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/param.h... yes
checking whether _XOPEN_SOURCE is declared... no
checking whether __get_cpuid_max is declared... yes
checking whether __cpuid_count is declared... yes
checking for x86intrin.h... yes
checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt
checking C compiler flags needed for avx2... -mavx2 -mpopcnt
checking C compiler flags needed for avx512f... -mavx512f -mpopcnt
checking for working __builtin_cpu_supports("ssse3")... yes
checking for working __attribute__((target("ssse3")))... yes
checking for x86_64-redhat-linux-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for gcc option to enable large file support... none needed
checking shared library type for x86_64-redhat-linux... plain .so
checking whether the linker supports versioned symbols... yes
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking for getauxval... yes
checking for elf_aux_info... no
checking for posix_memalign... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for __attribute__((constructor))... yes
checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes
checking for library containing dlsym... none required
checking whether the compiler accepts -rdynamic... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for fstatat... yes
checking for CMSG_LEN... yes
checking for epoll... yes (edge triggered)
checking for sendfile... yes, Linux-style
checking whether EHOSTDOWN is declared... yes
checking whether ENONET is declared... yes
checking whether AI_V4MAPPED is declared... yes
checking whether AI_ADDRCONFIG is declared... yes
checking whether the compiler accepts -Wextra... yes
checking whether the compiler accepts -Wformat... yes
checking whether the compiler accepts -Wformat=2... yes
checking whether the compiler accepts -Wconversion... yes
checking whether the compiler accepts -Wtrampolines... yes
checking whether the compiler accepts -Wstrict-aliasing... yes
checking whether the compiler accepts -fstack-clash-protection... yes
checking whether the compiler accepts -fstack-protector-strong... yes
checking whether the compiler accepts -fcf-protection=full... yes
checking whether the compiler accepts -mbranch-protection=standard... no
checking whether the compiler accepts -fno-delete-null-pointer-checks... yes
checking whether the compiler accepts -Wl,-z,noexecstack... yes
checking whether the compiler accepts -Wl,-z,relro... yes
checking whether the compiler accepts -Wl,-z,now... yes
checking whether the compiler accepts -Wl,--as-needed... yes
checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes
checking whether the compiler accepts -Wl,-z,nodlopen... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: linking htscodecs_bundled.mk to htscodecs.mk
configure: WARNING: unrecognized options: --disable-dependency-tracking
+ /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 -fvisibility=hidden  -I.  -c -o kfunc.o kfunc.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 -fvisibility=hidden  -I.  -c -o kstring.o kstring.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 -fvisibility=hidden  -I.  -c -o errmod.o errmod.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 -fvisibility=hidden  -I.  -c -o bcf_sr_sort.o bcf_sr_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 -fvisibility=hidden  -I.  -c -o faidx.o faidx.c
faidx.c: In function ‘fai_path’:
faidx.c:1042:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1042 |         char *fai_tmp = strstr(fa, HTS_IDX_DELIM);
      |                         ^~~~~~
echo '#define HTS_VERSION_TEXT "1.23"' > version.h
printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
'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 -fvisibility=hidden' \
'-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   -fvisibility=hidden -rdynamic' \
'-llzma -lbz2 -lz -lm ' > config_vars.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 -fvisibility=hidden  -I.  -c -o bgzf.o bgzf.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 -fvisibility=hidden  -I.  -c -o hts_os.o hts_os.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 -fvisibility=hidden  -I.  -c -o md5.o md5.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 -fvisibility=hidden  -I.  -c -o hfile.o hfile.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 -fvisibility=hidden  -I.  -c -o multipart.o multipart.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 -fvisibility=hidden  -I.  -c -o hts_expr.o hts_expr.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 -fvisibility=hidden  -I.  -c -o probaln.o probaln.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 -fvisibility=hidden  -I.  -c -o realn.o realn.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 -fvisibility=hidden  -I.  -c -o region.o region.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 -fvisibility=hidden  -I.  -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -I.  -c -o header.o header.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 -fvisibility=hidden  -I.  -c -o sam_mods.o sam_mods.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 -fvisibility=hidden  -I.  -c -o vcf_sweep.o vcf_sweep.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 -fvisibility=hidden  -I.  -c -o simd.o simd.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 -fvisibility=hidden  -I.  -c -o tbx.o tbx.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 -fvisibility=hidden  -I.  -c -o textutils.o textutils.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 -fvisibility=hidden  -I.  -c -o thread_pool.o thread_pool.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 -fvisibility=hidden  -I.  -c -o synced_bcf_reader.o synced_bcf_reader.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 -fvisibility=hidden  -I.  -c -o vcfutils.o vcfutils.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 -fvisibility=hidden  -I.  -c -o cram/cram_codecs.o cram/cram_codecs.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 -fvisibility=hidden  -I.  -c -o sam.o sam.c
sam.c: In function ‘sam_open_mode_opts’:
sam.c:5232:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 5232 |     if ((opts = strchr(format, ','))) {
      |               ^
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 -fvisibility=hidden  -I.  -c -o cram/cram_decode.o cram/cram_decode.c
cram/cram_decode.c: In function ‘cram_decode_seq’:
cram/cram_decode.c:1230:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1230 |                         char *N = memchr(refp, 'N', frag_len);
      |                                   ^~~~~~
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 -fvisibility=hidden  -I.  -c -o cram/cram_external.o cram/cram_external.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 -fvisibility=hidden  -I.  -c -o cram/cram_index.o cram/cram_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 -fvisibility=hidden  -I.  -c -o cram/cram_stats.o cram/cram_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 -fvisibility=hidden  -I.  -c -o cram/mFILE.o cram/mFILE.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 -fvisibility=hidden  -I.  -c -o cram/cram_encode.o cram/cram_encode.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 -fvisibility=hidden  -I.  -c -o cram/open_trace_file.o cram/open_trace_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 -fvisibility=hidden  -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.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 -fvisibility=hidden  -I.  -c -o cram/string_alloc.o cram/string_alloc.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 -fvisibility=hidden  -I.  -c -o vcf.o vcf.c
vcf.c: In function ‘bcf_get_version’:
vcf.c:167:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  167 |     if (!(major = strstr(version, vcf))) {  //bad format
      |                 ^
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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.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 -fvisibility=hidden  -I.  -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function ‘refs_load_fai’:
cram/cram_io.c:2557:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 2557 |     char *fn_delim = strstr(fn, HTS_IDX_DELIM);
      |                      ^~~~~~
cram/cram_io.c: In function ‘cram_dopen’:
cram/cram_io.c:5353:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 5353 |     fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename);
      |                             ^
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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.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 -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.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 -fvisibility=hidden -mavx512f -mpopcnt -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.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 -fvisibility=hidden -mavx2 -mpopcnt -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.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 -fvisibility=hidden  -I.  -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.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 -fvisibility=hidden  -I.  -fpic -c -o kfunc.pico kfunc.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.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 -fvisibility=hidden  -I.  -fpic -c -o kstring.pico kstring.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 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
htscodecs/htscodecs/tokenise_name3.c: In function ‘build_trie’:
htscodecs/htscodecs/tokenise_name3.c:478:9: warning: variable ‘nlines’ set but not used [-Wunused-but-set-variable=]
  478 |     int nlines = 0;
      |         ^~~~~~
htscodecs/htscodecs/tokenise_name3.c: In function ‘search_trie’:
htscodecs/htscodecs/tokenise_name3.c:592:9: warning: variable ‘nlines’ set but not used [-Wunused-but-set-variable=]
  592 |     int nlines = 0;
      |         ^~~~~~
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 -fvisibility=hidden  -I.  -fpic -c -o errmod.pico errmod.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 -fvisibility=hidden  -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_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 -fvisibility=hidden  -I.  -fpic -c -o faidx.pico faidx.c
faidx.c: In function ‘fai_path’:
faidx.c:1042:25: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1042 |         char *fai_tmp = strstr(fa, 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 -fvisibility=hidden  -I.  -fpic -c -o bgzf.pico bgzf.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 -fvisibility=hidden  -I.  -fpic -c -o hfile.pico hfile.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 -fvisibility=hidden  -I.  -fpic -c -o hts_os.pico hts_os.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 -fvisibility=hidden  -I.  -fpic -c -o md5.pico md5.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 -fvisibility=hidden  -I.  -fpic -c -o multipart.pico multipart.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 -fvisibility=hidden  -I.  -fpic -c -o hts_expr.pico hts_expr.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 -fvisibility=hidden  -I.  -fpic -c -o probaln.pico probaln.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 -fvisibility=hidden  -I.  -fpic -c -o realn.pico realn.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 -fvisibility=hidden  -I.  -fpic -c -o header.pico header.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 -fvisibility=hidden  -I.  -fpic -c -o region.pico region.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 -fvisibility=hidden  -I.  -fpic -c -o regidx.pico regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -I.  -fpic -c -o sam_mods.pico sam_mods.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 -fvisibility=hidden  -I.  -fpic -c -o simd.pico simd.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 -fvisibility=hidden  -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.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 -fvisibility=hidden  -I.  -fpic -c -o tbx.pico tbx.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 -fvisibility=hidden  -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.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 -fvisibility=hidden  -I.  -fpic -c -o textutils.pico textutils.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 -fvisibility=hidden  -I.  -fpic -c -o thread_pool.pico thread_pool.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 -fvisibility=hidden  -I.  -fpic -c -o hts.pico hts.c
hts.c: In function ‘hts_open_format’:
hts.c:941:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  941 |     char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM);
      |                                 ^~~~~~
hts.c: In function ‘hts_hopen’:
hts.c:1477:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1477 |     if ((cp = strchr(mode, ','))) {
      |             ^
hts.c: In function ‘reg2bins’:
hts.c:3183:12: warning: variable ‘t’ set but not used [-Wunused-but-set-variable=]
 3183 |     int l, t, s = min_shift + (n_lvls<<1) + n_lvls;
      |            ^
hts.c: In function ‘reg2intervals’:
hts.c:3301:12: warning: variable ‘t’ set but not used [-Wunused-but-set-variable=]
 3301 |     int l, t, s;
      |            ^
hts.c: In function ‘idx_find_and_load’:
hts.c:4922:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 4922 |     char *fnidx = 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 -fvisibility=hidden  -I.  -fpic -c -o vcfutils.pico vcfutils.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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.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 -fvisibility=hidden  -I.  -fpic -c -o sam.pico sam.c
sam.c: In function ‘sam_open_mode_opts’:
sam.c:5232:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 5232 |     if ((opts = strchr(format, ','))) {
      |               ^
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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
cram/cram_decode.c: In function ‘cram_decode_seq’:
cram/cram_decode.c:1230:35: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1230 |                         char *N = memchr(refp, 'N', frag_len);
      |                                   ^~~~~~
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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_index.pico cram/cram_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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_stats.pico cram/cram_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 -fvisibility=hidden  -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.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 -fvisibility=hidden  -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_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 -fvisibility=hidden  -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.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 -fvisibility=hidden  -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.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 -fvisibility=hidden  -I.  -fpic -c -o vcf.pico vcf.c
vcf.c: In function ‘bcf_get_version’:
vcf.c:167:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  167 |     if (!(major = strstr(version, vcf))) {  //bad format
      |                 ^
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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.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 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
cram/cram_io.c: In function ‘refs_load_fai’:
cram/cram_io.c:2557:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 2557 |     char *fn_delim = strstr(fn, HTS_IDX_DELIM);
      |                      ^~~~~~
cram/cram_io.c: In function ‘cram_dopen’:
cram/cram_io.c:5353:29: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 5353 |     fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename);
      |                             ^
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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.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 -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.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 -fvisibility=hidden -mavx512f -mpopcnt -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.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 -fvisibility=hidden -mavx2 -mpopcnt -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.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 -fvisibility=hidden  -I.  -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.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 -fvisibility=hidden  -I.  -c -o htsfile.o htsfile.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 -fvisibility=hidden  -I.  -c -o bgzip.o bgzip.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 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
htscodecs/htscodecs/tokenise_name3.c: In function ‘build_trie’:
htscodecs/htscodecs/tokenise_name3.c:478:9: warning: variable ‘nlines’ set but not used [-Wunused-but-set-variable=]
  478 |     int nlines = 0;
      |         ^~~~~~
htscodecs/htscodecs/tokenise_name3.c: In function ‘search_trie’:
htscodecs/htscodecs/tokenise_name3.c:592:9: warning: variable ‘nlines’ set but not used [-Wunused-but-set-variable=]
  592 |     int nlines = 0;
      |         ^~~~~~
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 -fvisibility=hidden  -I.  -fpic -c -o hfile_gcs.pico hfile_gcs.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 -fvisibility=hidden  -I.  -c -o annot-tsv.o annot-tsv.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 -fvisibility=hidden  -I.  -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -I.  -c -o test/fieldarith.o test/fieldarith.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 -fvisibility=hidden  -I.  -c -o test/hts_endian.o test/hts_endian.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 -fvisibility=hidden  -I.  -c -o test/hfile.o test/hfile.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 -fvisibility=hidden  -I.  -c -o test/pileup.o test/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 -fvisibility=hidden  -I.  -fpic -c -o hfile_libcurl.pico hfile_libcurl.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 -fvisibility=hidden  -I.  -c -o test/plugins-dlhts.o test/plugins-dlhts.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 -fvisibility=hidden  -I.  -c -o test/pileup_mod.o test/pileup_mod.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 -fvisibility=hidden  -I.  -c -o test/test_expr.o test/test_expr.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 -fvisibility=hidden  -I.  -c -o test/test_faidx.o test/test_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 -fvisibility=hidden  -I.  -c -o test/test_kfunc.o test/test_kfunc.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 -fvisibility=hidden  -I.  -c -o test/test_bgzf.o test/test_bgzf.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 -fvisibility=hidden  -I.  -fpic -c -o hfile_s3.pico hfile_s3.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 -fvisibility=hidden  -I.  -c -o test/test_mod.o test/test_mod.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 -fvisibility=hidden  -I.  -c -o test/test_khash.o test/test_khash.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 -fvisibility=hidden  -I.  -c -o test/test_kstring.o test/test_kstring.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 -fvisibility=hidden  -I.  -c -o test/test_nibbles.o test/test_nibbles.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 -fvisibility=hidden  -I.  -c -o test/test_realn.o test/test_realn.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 -fvisibility=hidden  -I.  -c -o test/sam.o test/sam.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 -fvisibility=hidden  -I.  -c -o test/test_time_funcs.o test/test_time_funcs.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 -fvisibility=hidden  -I.  -c -o test/test_index.o test/test_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 -fvisibility=hidden  -I.  -c -o test/test_str2int.o test/test_str2int.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 -fvisibility=hidden  -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -I.  -c -o test/test_view.o test/test_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 -fvisibility=hidden  -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.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 -fvisibility=hidden  -I.  -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.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 -fvisibility=hidden  -I.  -c -o test/test-bcf-translate.o test/test-bcf-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 -fvisibility=hidden  -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.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 -fvisibility=hidden  -I.  -c -o test/test_introspection.o test/test_introspection.c
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc
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 -fvisibility=hidden  -I.  -c -o test/test-parse-reg.o test/test-parse-reg.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/listener.o ref_cache/listener.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 -fvisibility=hidden  -I.  -c -o test/test-vcf-api.o test/test-vcf-api.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/log_files.o ref_cache/log_files.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/http_parser.o ref_cache/http_parser.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/misc.o ref_cache/misc.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/ping.o ref_cache/ping.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/request_handler.o ref_cache/request_handler.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/ref_files.o ref_cache/ref_files.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/main.o ref_cache/main.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/transaction.o ref_cache/transaction.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/server.o ref_cache/server.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 -fvisibility=hidden -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks  -I.  -c -o ref_cache/upstream.o ref_cache/upstream.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   -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm 
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   -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm 
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 -fvisibility=hidden  -I.  -c -o hts.o hts.c
hts.c: In function ‘hts_open_format’:
hts.c:941:33: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  941 |     char *rmme = NULL, *fnidx = strstr(fn, HTS_IDX_DELIM);
      |                                 ^~~~~~
hts.c: In function ‘hts_hopen’:
hts.c:1477:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1477 |     if ((cp = strchr(mode, ','))) {
      |             ^
hts.c: In function ‘reg2bins’:
hts.c:3183:12: warning: variable ‘t’ set but not used [-Wunused-but-set-variable=]
 3183 |     int l, t, s = min_shift + (n_lvls<<1) + n_lvls;
      |            ^
hts.c: In function ‘reg2intervals’:
hts.c:3301:12: warning: variable ‘t’ set but not used [-Wunused-but-set-variable=]
 3301 |     int l, t, s;
      |            ^
hts.c: In function ‘idx_find_and_load’:
hts.c:4922:19: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 4922 |     char *fnidx = strstr(fn, HTS_IDX_DELIM);
      |                   ^~~~~~
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   -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o  plugin.o
ranlib libhts.a
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 -fvisibility=hidden  -I.  -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c
In file included from test/test-bcf_set_variant_type.c:30:
test/../vcf.c: In function ‘bcf_get_version’:
test/../vcf.c:167:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  167 |     if (!(major = strstr(version, vcf))) {  //bad format
      |                 ^
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   -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl
gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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   -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico plugin.pico -llzma -lbz2 -lz -lm  -lpthread
ln -sf libhts.so libhts.so.3
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   -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
gcc -shared -Wl,-E -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   -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm  -lcurl -lpthread
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   -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
gcc -shared -Wl,-E -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   -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm  -lpthread
gcc -shared -Wl,-E -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   -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm  -lcrypto -lcurl -lpthread
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   -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
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   -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm  -lpthread
+ sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.FawUnk
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.23-build
+ '[' /builddir/build/BUILD/htslib-1.23-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/htslib-1.23-build/BUILDROOT
++ dirname /builddir/build/BUILD/htslib-1.23-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/htslib-1.23-build
+ mkdir /builddir/build/BUILD/htslib-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 htslib-1.23
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/htslib-1.23-build/BUILDROOT 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/bin /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/include /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/include/htslib /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man5 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man7 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/pkgconfig
if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/libexec/htslib; fi
/usr/bin/install -p -m 644 libhts.so /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.so.1.23
ln -sf libhts.so.1.23 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.so
ln -sf libhts.so.1.23 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.so.3
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.23#g' htslib.pc.tmp > /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc
chmod 644 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc
/usr/bin/install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/bin
if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/libexec/htslib; fi
/usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/include/htslib
/usr/bin/install -p -m 644 libhts.a /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64/libhts.a
/usr/bin/install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man1
if test "xref_cache/ref-cache" != "x" ; then \
    /usr/bin/install -p -m 644 ref_cache/ref-cache.1 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man1 ; \
fi
/usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man5
/usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/man/man7
+ pushd /builddir/build/BUILD/htslib-1.23-build/BUILDROOT//usr/lib64
~/build/BUILD/htslib-1.23-build/BUILDROOT/usr/lib64 ~/build/BUILD/htslib-1.23-build/htslib-1.23
+ chmod 755 libhts.so.1.23
+ popd
~/build/BUILD/htslib-1.23-build/htslib-1.23
+ find /builddir/build/BUILD/htslib-1.23-build/BUILDROOT -name '*.la' -delete
+ rm -f /builddir/build/BUILD/htslib-1.23-build/BUILDROOT//usr/lib64/libhts.a
+ /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 htslib-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/htslib-1.23-build/htslib-1.23
find-debuginfo: starting
Extracting debug info from 9 files
DWARF-compressing 9 files
sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-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/htslib-1.23-build/BUILDROOT
Scanned 30 directories and 209 files,
    processed 9 inodes,
    0 modified (0 replaced + 0 rewritten),
    0 unsupported format, 0 errors
+ /usr/bin/linkdupes --brp /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr
Scanned 29 directories and 209 files,
    considered 207 files, read 42 files, linked 21 files, 0 errors
    sum of sizes of linked files: 426081 bytes
Reading /builddir/build/BUILD/htslib-1.23-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.JiClgd
+ umask 022
+ cd /builddir/build/BUILD/htslib-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 htslib-1.23
+ make test
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc
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 -fvisibility=hidden  -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.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   -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm  -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test
Testing rans4x8 -r -o0 on ./dat/q4	11674
Testing rans4x8 -r -o1 on ./dat/q4	10870
Testing rans4x8 -r -o0 on ./dat/q40+dir	50258
Testing rans4x8 -r -o1 on ./dat/q40+dir	50537
Testing rans4x8 -r -o0 on ./dat/q8	33099
Testing rans4x8 -r -o1 on ./dat/q8	31428
Testing rans4x8 -r -o0 on ./dat/qvar	32997
Testing rans4x8 -r -o1 on ./dat/qvar	32832
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 -fvisibility=hidden  -I. -Ihtscodecs -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.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   -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm  -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test
Testing rans4x16 -r -o0 on ./dat/q4	11660
Testing rans4x16 -r -o1 on ./dat/q4	10848
Testing rans4x16 -r -o64 on ./dat/q4	12878
Testing rans4x16 -r -o65 on ./dat/q4	10672
Testing rans4x16 -r -o128 on ./dat/q4	10902
Testing rans4x16 -r -o129 on ./dat/q4	10890
Testing rans4x16 -r -o192 on ./dat/q4	11225
Testing rans4x16 -r -o193 on ./dat/q4	10825
Testing rans4x16 -r -o8 on ./dat/q4	11731
Testing rans4x16 -r -o9 on ./dat/q4	11111
Testing rans4x16 -r -o4 on ./dat/q4	11746
11746
11746
11746
Testing rans4x16 -r -o5 on ./dat/q4	10932
10932
10932
10932
Testing rans4x16 -r -o0 on ./dat/q40+dir	50247
Testing rans4x16 -r -o1 on ./dat/q40+dir	49449
Testing rans4x16 -r -o8 on ./dat/q40+dir	50072
Testing rans4x16 -r -o9 on ./dat/q40+dir	50072
Testing rans4x16 -r -o4 on ./dat/q40+dir	50331
50331
50331
50331
Testing rans4x16 -r -o5 on ./dat/q40+dir	49537
49537
49537
49537
Testing rans4x16 -r -o0 on ./dat/q8	33088
Testing rans4x16 -r -o1 on ./dat/q8	31372
Testing rans4x16 -r -o64 on ./dat/q8	33458
Testing rans4x16 -r -o65 on ./dat/q8	31025
Testing rans4x16 -r -o128 on ./dat/q8	32237
Testing rans4x16 -r -o129 on ./dat/q8	31258
Testing rans4x16 -r -o192 on ./dat/q8	32024
Testing rans4x16 -r -o193 on ./dat/q8	31146
Testing rans4x16 -r -o4 on ./dat/q8	33176
33176
33176
33176
Testing rans4x16 -r -o5 on ./dat/q8	31458
31458
31458
31458
Testing rans4x16 -r -o69 on ./dat/qsimd	35
Testing rans4x16 -r -o4 on ./dat/qsimd	219
219
219
219
Testing rans4x16 -r -o5 on ./dat/qsimd	151
151
151
151
Testing rans4x16 -r -o0 on ./dat/qvar	32987
Testing rans4x16 -r -o1 on ./dat/qvar	32261
Testing rans4x16 -r -o4 on ./dat/qvar	33073
33073
33073
33073
Testing rans4x16 -r -o5 on ./dat/qvar	32353
32353
32353
32353
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 -fvisibility=hidden  -I. -Ihtscodecs -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.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   -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm  -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test
Testing arith_dynamic -r -o0 on ./dat/q4	11615
Testing arith_dynamic -r -o1 on ./dat/q4	10831
Testing arith_dynamic -r -o64 on ./dat/q4	13360
Testing arith_dynamic -r -o65 on ./dat/q4	10484
Testing arith_dynamic -r -o128 on ./dat/q4	10774
Testing arith_dynamic -r -o129 on ./dat/q4	10329
Testing arith_dynamic -r -o192 on ./dat/q4	11095
Testing arith_dynamic -r -o193 on ./dat/q4	10283
Testing arith_dynamic -r -o8 on ./dat/q4	11448
Testing arith_dynamic -r -o9 on ./dat/q4	11083
Testing arith_dynamic -r -o0 on ./dat/q40+dir	49949
Testing arith_dynamic -r -o1 on ./dat/q40+dir	49034
Testing arith_dynamic -r -o64 on ./dat/q40+dir	51242
Testing arith_dynamic -r -o65 on ./dat/q40+dir	49061
Testing arith_dynamic -r -o8 on ./dat/q40+dir	49820
Testing arith_dynamic -r -o9 on ./dat/q40+dir	49448
Testing arith_dynamic -r -o0 on ./dat/q8	32752
Testing arith_dynamic -r -o1 on ./dat/q8	31331
Testing arith_dynamic -r -o64 on ./dat/q8	35211
Testing arith_dynamic -r -o65 on ./dat/q8	30907
Testing arith_dynamic -r -o128 on ./dat/q8	32063
Testing arith_dynamic -r -o129 on ./dat/q8	31084
Testing arith_dynamic -r -o192 on ./dat/q8	32267
Testing arith_dynamic -r -o193 on ./dat/q8	30931
Testing arith_dynamic -r -o0 on ./dat/qvar	32597
Testing arith_dynamic -r -o1 on ./dat/qvar	31982
Testing arith_dynamic -r -o64 on ./dat/qvar	33237
Testing arith_dynamic -r -o65 on ./dat/qvar	31993
Testing arith_dynamic -r -o1 on ./dat/u32	27005
Testing arith_dynamic -r -o65 on ./dat/u32	23864
Testing arith_dynamic -r -o9 on ./dat/u32	24811
Testing arith_dynamic -r -o4 on ./dat/u32	20849
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 -fvisibility=hidden  -I. -Ihtscodecs -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.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   -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm  -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test
Testing tokenise_name3 -r -1 on ./names/01.names	2708
Testing tokenise_name3 -r -3 on ./names/01.names	2429
Testing tokenise_name3 -r -5 on ./names/01.names	2264
Testing tokenise_name3 -r -7 on ./names/01.names	2264
Testing tokenise_name3 -r -9 on ./names/01.names	2234
Testing tokenise_name3 -r -11 on ./names/01.names	2449
Testing tokenise_name3 -r -13 on ./names/01.names	2085
Testing tokenise_name3 -r -15 on ./names/01.names	2071
Testing tokenise_name3 -r -17 on ./names/01.names	2070
Testing tokenise_name3 -r -19 on ./names/01.names	2051

Testing tokenise_name3 -r -1 on ./names/02.names	5390
Testing tokenise_name3 -r -3 on ./names/02.names	4955
Testing tokenise_name3 -r -5 on ./names/02.names	4923
Testing tokenise_name3 -r -7 on ./names/02.names	4923
Testing tokenise_name3 -r -9 on ./names/02.names	4918
Testing tokenise_name3 -r -11 on ./names/02.names	4838
Testing tokenise_name3 -r -13 on ./names/02.names	4757
Testing tokenise_name3 -r -15 on ./names/02.names	4743
Testing tokenise_name3 -r -17 on ./names/02.names	4716
Testing tokenise_name3 -r -19 on ./names/02.names	4700

Testing tokenise_name3 -r -1 on ./names/03.names	8854
Testing tokenise_name3 -r -3 on ./names/03.names	7782
Testing tokenise_name3 -r -5 on ./names/03.names	7771
Testing tokenise_name3 -r -7 on ./names/03.names	7771
Testing tokenise_name3 -r -9 on ./names/03.names	7521
Testing tokenise_name3 -r -11 on ./names/03.names	7395
Testing tokenise_name3 -r -13 on ./names/03.names	7252
Testing tokenise_name3 -r -15 on ./names/03.names	7252
Testing tokenise_name3 -r -17 on ./names/03.names	7225
Testing tokenise_name3 -r -19 on ./names/03.names	7075

Testing tokenise_name3 -r -1 on ./names/05.names	3787
Testing tokenise_name3 -r -3 on ./names/05.names	3564
Testing tokenise_name3 -r -5 on ./names/05.names	3536
Testing tokenise_name3 -r -7 on ./names/05.names	3536
Testing tokenise_name3 -r -9 on ./names/05.names	3534
Testing tokenise_name3 -r -11 on ./names/05.names	3411
Testing tokenise_name3 -r -13 on ./names/05.names	3397
Testing tokenise_name3 -r -15 on ./names/05.names	3383
Testing tokenise_name3 -r -17 on ./names/05.names	3383
Testing tokenise_name3 -r -19 on ./names/05.names	3377

Testing tokenise_name3 -r -1 on ./names/08.names	5579
Testing tokenise_name3 -r -3 on ./names/08.names	5274
Testing tokenise_name3 -r -5 on ./names/08.names	5246
Testing tokenise_name3 -r -7 on ./names/08.names	5213
Testing tokenise_name3 -r -9 on ./names/08.names	5160
Testing tokenise_name3 -r -11 on ./names/08.names	4915
Testing tokenise_name3 -r -13 on ./names/08.names	4901
Testing tokenise_name3 -r -15 on ./names/08.names	4887
Testing tokenise_name3 -r -17 on ./names/08.names	4844
Testing tokenise_name3 -r -19 on ./names/08.names	4805

Testing tokenise_name3 -r -1 on ./names/09.names	3740
Testing tokenise_name3 -r -3 on ./names/09.names	3539
Testing tokenise_name3 -r -5 on ./names/09.names	3539
Testing tokenise_name3 -r -7 on ./names/09.names	3528
Testing tokenise_name3 -r -9 on ./names/09.names	3493
Testing tokenise_name3 -r -11 on ./names/09.names	3431
Testing tokenise_name3 -r -13 on ./names/09.names	3394
Testing tokenise_name3 -r -15 on ./names/09.names	3394
Testing tokenise_name3 -r -17 on ./names/09.names	3386
Testing tokenise_name3 -r -19 on ./names/09.names	3366

Testing tokenise_name3 -r -1 on ./names/10.names	5210
Testing tokenise_name3 -r -3 on ./names/10.names	4782
Testing tokenise_name3 -r -5 on ./names/10.names	4752
Testing tokenise_name3 -r -7 on ./names/10.names	4752
Testing tokenise_name3 -r -9 on ./names/10.names	4744
Testing tokenise_name3 -r -11 on ./names/10.names	4566
Testing tokenise_name3 -r -13 on ./names/10.names	4520
Testing tokenise_name3 -r -15 on ./names/10.names	4506
Testing tokenise_name3 -r -17 on ./names/10.names	4494
Testing tokenise_name3 -r -19 on ./names/10.names	4476

Testing tokenise_name3 -r -1 on ./names/20.names	1783
Testing tokenise_name3 -r -3 on ./names/20.names	1668
Testing tokenise_name3 -r -5 on ./names/20.names	1640
Testing tokenise_name3 -r -7 on ./names/20.names	1640
Testing tokenise_name3 -r -9 on ./names/20.names	1632
Testing tokenise_name3 -r -11 on ./names/20.names	1645
Testing tokenise_name3 -r -13 on ./names/20.names	1625
Testing tokenise_name3 -r -15 on ./names/20.names	1611
Testing tokenise_name3 -r -17 on ./names/20.names	1609
Testing tokenise_name3 -r -19 on ./names/20.names	1600

Testing tokenise_name3 -r -1 on ./names/nv.names	5273
Testing tokenise_name3 -r -3 on ./names/nv.names	4968
Testing tokenise_name3 -r -5 on ./names/nv.names	4941
Testing tokenise_name3 -r -7 on ./names/nv.names	4941
Testing tokenise_name3 -r -9 on ./names/nv.names	4937
Testing tokenise_name3 -r -11 on ./names/nv.names	4864
Testing tokenise_name3 -r -13 on ./names/nv.names	4785
Testing tokenise_name3 -r -15 on ./names/nv.names	4772
Testing tokenise_name3 -r -17 on ./names/nv.names	4772
Testing tokenise_name3 -r -19 on ./names/nv.names	4767

Testing tokenise_name3 -r -1 on ./names/nv2.names	1060
Testing tokenise_name3 -r -3 on ./names/nv2.names	891
Testing tokenise_name3 -r -5 on ./names/nv2.names	863
Testing tokenise_name3 -r -7 on ./names/nv2.names	863
Testing tokenise_name3 -r -9 on ./names/nv2.names	855
Testing tokenise_name3 -r -11 on ./names/nv2.names	836
Testing tokenise_name3 -r -13 on ./names/nv2.names	799
Testing tokenise_name3 -r -15 on ./names/nv2.names	785
Testing tokenise_name3 -r -17 on ./names/nv2.names	779
Testing tokenise_name3 -r -19 on ./names/nv2.names	767

Testing tokenise_name3 -r -1 on ./names/rr.names	6605
Testing tokenise_name3 -r -3 on ./names/rr.names	6237
Testing tokenise_name3 -r -5 on ./names/rr.names	6237
Testing tokenise_name3 -r -7 on ./names/rr.names	6237
Testing tokenise_name3 -r -9 on ./names/rr.names	6230
Testing tokenise_name3 -r -11 on ./names/rr.names	6151
Testing tokenise_name3 -r -13 on ./names/rr.names	6025
Testing tokenise_name3 -r -15 on ./names/rr.names	6025
Testing tokenise_name3 -r -17 on ./names/rr.names	6023
Testing tokenise_name3 -r -19 on ./names/rr.names	5973

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 -fvisibility=hidden  -I. -Ihtscodecs -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.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   -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm  -lm -lpthread
cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test





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 -fvisibility=hidden  -I. -Ihtscodecs -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.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   -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o -llzma -lbz2 -lz -lm  -lm -lpthread
cd htscodecs/tests && ./varint
test/hts_endian
test/test_expr
test/test_kfunc
test/test_khash
test/test_kstring
test/test_nibbles -v
test/test_str2int
test/test_time_funcs
test/fieldarith test/fieldarith.sam
test/hfile
if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \
    HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \
fi
if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \
  HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \
fi
test/test_bgzf test/bgziptest.txt
test/test-parse-reg -t test/colons.bam
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead
Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead
Expected error: [E::hts_parse_region] Mismatching braces in "{chr1"
Expected error: [E::hts_parse_region] Unexpected string "x" after region
Expected error: [E::hts_parse_region] Unexpected string "y" after region
Expected error: [E::hts_parse_region] Unexpected string "chr3" after region
cd test/faidx && ./test-faidx.sh faidx.tst
Testing faidx...
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5
PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90
PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90
PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai
PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225

Expected   passes:   25
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
cd test/sam_filter && ./filter.sh filter.tst
Testing sam_filter...
PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam
PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam
PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam
PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam
PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam
PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam
PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@'
PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@'
PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@'
PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@'
PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@'

Expected   passes:   18
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
cd test/tabix && ./test-tabix.sh tabix.tst
Testing tabix...
PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz
PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151
PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812
PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero)
PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz
PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz
PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200
PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz
PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190
PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005
PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2
PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2

Expected   passes:   16
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
cd test/mpileup && ./test-pileup.sh mpileup.tst
Testing (m)pileup...
PASS : $pileup mp_D.sam
PASS : $pileup -m mp_D.sam
PASS : $pileup mp_DI.sam
PASS : $pileup -m mp_DI.sam
PASS : $pileup mp_I.sam
PASS : $pileup -m mp_I.sam
PASS : $pileup mp_P.sam
PASS : $pileup -m mp_P.sam
PASS : $pileup mp_ID.sam
PASS : $pileup -m mp_ID.sam
PASS : $pileup mp_N.sam
PASS : $pileup -m mp_N.sam
PASS : $pileup mp_N2.sam
PASS : $pileup -m mp_N2.sam
PASS : $pileup c1#pad1.sam
PASS : $pileup -m c1#pad1.sam
PASS : $pileup c1#pad2.sam
PASS : $pileup -m c1#pad2.sam
PASS : $pileup c1#pad3.sam
PASS : $pileup -m c1#pad3.sam
PASS : $pileup -m small.bam
PASS : $pileup -m mp_overlap1.sam
PASS : $pileup -m mp_overlap2.sam

Expected   passes:   23
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
cd test/fastq && ./test-fastq.sh
Testing fastq support
PASS : $tview minimal.fq
PASS : $tview minimal.fa
PASS : $tview multiline.fq
PASS : $tview multiline.fa
PASS : $tview -i fastq_aux longline.fq
PASS : $tview single.fq
PASS : $tview single.fa
PASS : $tview -i fastq_aux single.fq
PASS : $tview -i fastq_aux single.fa
PASS : $tview interleaved.fq
PASS : $tview interleaved.fa
PASS : $tview -i fastq_aux interleaved.fq
PASS : $tview -i fastq_aux interleaved.fa
PASS : $tview -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq
PASS : $tview -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa
PASS : $tview -i fastq_casava filter_casava.fq
PASS : $tview -i fastq_casava filter_casava.fa
PASS : $tview -i fastq_aux r1.fq
PASS : $tview -i fastq_aux r2.fq
PASS : $tview -i fastq_aux r1.fa
PASS : $tview -i fastq_aux r2.fa
PASS : $tview -i fastq_name2 name2.fq
PASS : $tview -i fastq_name2 name2.fa
PASS : $tview -i fastq_umi=RX UMI.fq
PASS : $tview -f minimal.sam
PASS : $tview -F minimal.sam
PASS : $tview -f -o fastq_aux single_aux.sam
PASS : $tview -F -o fastq_aux single_aux.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam
PASS : $tview -f -o fastq_casava inter_casava.sam
PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -F -o fastq_casava inter_casava.sam
PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam
PASS : $tview -f -o fastq_casava filter_casava.sam
PASS : $tview -F -o fastq_casava filter_casava.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam
PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam
PASS : $tview -f -o fastq_rnum -o fastq_umi UMI.sam

Expected   passes:   43
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
cd test/base_mods && ./base-mods.sh base-mods.tst
Testing base-modifications...
PASS : $test_mod MM-chebi.sam
PASS : $test_mod MM-double.sam
PASS : $test_mod MM-multi.sam
PASS : $test_mod MM-explicit.sam
PASS : $test_mod -x MM-explicit.sam
PASS : $test_mod -f 1 MM-explicit.sam
PASS : $test_mod MM-not-all-modded.sam
PASS : $pileup_mod < MM-pileup.sam
PASS : $pileup_mod < MM-pileup2.sam
PASS : $pileup_mod < MM-MNp.sam
PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero)
PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero)
PASS : $test_mod < MM-MNf1.sam (must exit non-zero)
PASS : $test_mod < MM-MNf2.sam (must exit non-zero)
PASS : $test_mod < MM-bounds+.sam (must exit non-zero)
PASS : $test_mod < MM-bounds-.sam (must exit non-zero)
PASS : $test_mod -f 1 MM-variants.sam

Expected   passes:   17
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
cd test/tlen && ./tlen.sh tlen.tst
Testing CRAM TLEN auto-creation...
PASS : $test_view a7.cram
PASS : $test_view a7b.cram
PASS : $test_view a8.cram
PASS : $test_view a8b.cram
PASS : $test_view a9.cram
PASS : $test_view a9b.cram
PASS : $test_view b7.cram
PASS : $test_view b7b.cram
PASS : $test_view b8.cram
PASS : $test_view b8b.cram
PASS : $test_view c7.cram
PASS : $test_view c7b.cram
PASS : $test_view c8.cram
PASS : $test_view c8b.cram
PASS : $test_view d7.cram
PASS : $test_view d7b.cram
PASS : $test_view d4.cram
PASS : $test_view d4b.cram
PASS : $test_view d4c.cram
PASS : $test_view d4d.cram
PASS : $test_view d4e.cram
PASS : $test_view d4f.cram
PASS : $test_view d5.cram
PASS : $test_view d5b.cram
PASS : $test_view d5c.cram
PASS : $test_view d5d.cram
PASS : $test_view d5e.cram
PASS : $test_view d5f.cram
PASS : $test_view a4.cram
PASS : $test_view a5.cram

Expected   passes:   30
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq
(Expect trailing 'x' message for " 	 -1,001x")
[W::hts_parse_decimal] Ignoring unknown characters after -1,001[x]
(Expect trailing 'k' message for "1.5e+3k")
[W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k]
(Expect dropped fraction message for "12.3456k")
[W::hts_parse_decimal] Discarding fractional part of 12.3456k
[W::hts_parse_decimal] Discarding fractional part of 12.3456k
(Expect invalid numeric message for "A")
[W::hts_parse_decimal] Invalid numeric value A[truncated]
(Expect invalid numeric message for "G")
[W::hts_parse_decimal] Invalid numeric value G[truncated]
(Expect invalid numeric message for " +/-")
[W::hts_parse_decimal] Invalid numeric value +/-[truncated]
(Expect invalid numeric message for " 	 -.e+9999")
[W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated]
test/test-regidx
cd test && \
if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so" != "x"; then \
  REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \
else \
  REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \
fi
bgzip round-trip no threads: .. ok

bgzip text mode round-trip no threads: .. ok

bgzip -b no threads: .. ok

bgzip -b -I no threads: .. ok

bgzip multifile no threads: .. ok

bgzip --output no threads: .. ok

bgzip round-trip  4 threads: .. ok

bgzip text mode round-trip  4 threads: .. ok

bgzip -b  4 threads: .. ok

bgzip -b -I  4 threads: .. ok

bgzip multifile  4 threads: .. ok

bgzip --output  4 threads: .. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -b -m 14 -x /tmp/q3ZAyExF5w/index.bam.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -b -m 0 -x /tmp/q3ZAyExF5w/index.bam.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -z -m 14 -x /tmp/q3ZAyExF5w/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -z -m 0 -x /tmp/q3ZAyExF5w/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -z -m 14 -x /tmp/q3ZAyExF5w/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -z -m 0 -x /tmp/q3ZAyExF5w/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -C -x /tmp/q3ZAyExF5w/index.cram.crai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.cram
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index /tmp/q3ZAyExF5w/index.cram
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -p /tmp/q3ZAyExF5w/index3_rgn.sam /tmp/q3ZAyExF5w/index3.cram CHROMOSOME_I:5000-5100
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -M -p /tmp/q3ZAyExF5w/index3_rgnm.sam /tmp/q3ZAyExF5w/index3.cram CHROMOSOME_I:5000-5100
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -b -m 14 -x /tmp/q3ZAyExF5w/index.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/q3ZAyExF5w/index.bcf
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.bcf
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -z -m 14 -x /tmp/q3ZAyExF5w/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -l 0 -z -m 0 -x /tmp/q3ZAyExF5w/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -t /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/tabix /tmp/q3ZAyExF5w/index.vcf.gz##idx##/tmp/q3ZAyExF5w/index.vcf.gz.tbi 1:10000060-10000060
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 1:1000000-1000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 1:2000000-2000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 2:1000000-1000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 2:2000000-2000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/q3ZAyExF5w/index.bam.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -b -m 0 -x /tmp/q3ZAyExF5w/index.bam.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/q3ZAyExF5w/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/q3ZAyExF5w/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/q3ZAyExF5w/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/q3ZAyExF5w/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/q3ZAyExF5w/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/q3ZAyExF5w/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -C -x /tmp/q3ZAyExF5w/index.cram.crai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/q3ZAyExF5w/index.cram
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index /tmp/q3ZAyExF5w/index.cram
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -p /tmp/q3ZAyExF5w/index3_rgn.sam /tmp/q3ZAyExF5w/index3.cram CHROMOSOME_I:5000-5100
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -M -p /tmp/q3ZAyExF5w/index3_rgnm.sam /tmp/q3ZAyExF5w/index3.cram CHROMOSOME_I:5000-5100
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -b -m 14 -x /tmp/q3ZAyExF5w/index.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/q3ZAyExF5w/index.bcf
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.bcf
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 14 -x /tmp/q3ZAyExF5w/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -l 0 -z -m 0 -x /tmp/q3ZAyExF5w/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -t /tmp/q3ZAyExF5w/index.vcf.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/tabix /tmp/q3ZAyExF5w/index.vcf.gz##idx##/tmp/q3ZAyExF5w/index.vcf.gz.tbi 1:10000060-10000060
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 1:1000000-1000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 1:2000000-2000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 2:1000000-1000000
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/q3ZAyExF5w/index2.bam 2:2000000-2000000
.. ok

test_view testing multi-ref CRAM modes:
  ./test_view  -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view  multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view  -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view  multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view  -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view  multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok

test_view testing multi-ref CRAM modes:
  ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
  ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram
  ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_
  ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_
.. ok

test_view testing auxf#values.sam, ref auxf.fa:
  ./test_view  -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view  auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view  -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
  ./test_view  -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view  -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view  auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view  -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok

test_view testing c1#bounds.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
  ./test_view  c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
  ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
  ./test_view  -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
  ./test_view  c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#clip.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
  ./test_view  c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
  ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
  ./test_view  -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
  ./test_view  c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#noseq.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
  ./test_view  c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
  ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
  ./test_view  -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
  ./test_view  c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#pad1.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
  ./test_view  c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
  ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
  ./test_view  -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
  ./test_view  c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#pad2.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
  ./test_view  c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
  ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
  ./test_view  -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
  ./test_view  c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#pad3.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
  ./test_view  c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
  ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view  -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
  ./test_view  c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#unknown.sam, ref c1.fa:
  ./test_view  -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
  ./test_view  c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
  ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
  ./test_view  -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
  ./test_view  -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
  ./test_view  -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
  ./test_view  c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
.. ok

test_view testing c2#pad.sam, ref c2.fa:
  ./test_view  -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
  ./test_view  c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
  ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
  ./test_view  -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
  ./test_view  -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
  ./test_view  -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
  ./test_view  c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#1.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#1.sam > ce#1.tmp.bam
  ./test_view  ce#1.tmp.bam > ce#1.tmp.bam.sam_
  ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
  ./test_view  -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
  ./test_view  ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#1000.sam, ref ce.fa:
  ./test_view  -S -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view  ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view  -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view  ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
  ./test_view  -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view  -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
  ./test_view  -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
  ./test_view  ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#2.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#2.sam > ce#2.tmp.bam
  ./test_view  ce#2.tmp.bam > ce#2.tmp.bam.sam_
  ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
  ./test_view  -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
  ./test_view  ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#5.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#5.sam > ce#5.tmp.bam
  ./test_view  ce#5.tmp.bam > ce#5.tmp.bam.sam_
  ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
  ./test_view  -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
  ./test_view  ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#5b.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
  ./test_view  ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
  ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
  ./test_view  -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
  ./test_view  ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
  ./test_view  -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok

test_view testing ce#large_seq.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
  ./test_view  ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
  ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view  -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
  ./test_view  ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#supp.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
  ./test_view  ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
  ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
  ./test_view  -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
  ./test_view  ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#tag_depadded.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
  ./test_view  ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
  ./test_view  -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
  ./test_view  ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#tag_padded.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
  ./test_view  ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
  ./test_view  -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
  ./test_view  ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#unmap.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
  ./test_view  ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
  ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
  ./test_view  -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
  ./test_view  ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#unmap1.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
  ./test_view  ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
  ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
  ./test_view  -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
  ./test_view  ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#unmap2.sam, ref ce.fa:
  ./test_view  -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
  ./test_view  ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
  ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
  ./test_view  -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
  ./test_view  -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
  ./test_view  -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
  ./test_view  ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
.. ok

test_view testing md#1.sam, ref md.fa:
  ./test_view  -S -l0 -b md#1.sam > md#1.tmp.bam
  ./test_view  md#1.tmp.bam > md#1.tmp.bam.sam_
  ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
  ./test_view  -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
  ./test_view  -D md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
  ./test_view  -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
  ./test_view  md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#blank.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
  ./test_view  xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
  ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
  ./test_view  -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
  ./test_view  xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#large_aux.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
  ./test_view  xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view  -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
  ./test_view  xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
  ./test_view  -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
  ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok

test_view testing xx#large_aux2.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
  ./test_view  xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
  ./test_view  -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
  ./test_view  xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#MD.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
  ./test_view  xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
  ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
  ./test_view  -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
  ./test_view  xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#MD2.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
  ./test_view  xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view  -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
  ./test_view  xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#minimal.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
  ./test_view  xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
  ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
  ./test_view  -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
  ./test_view  xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#pair.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
  ./test_view  xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
  ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
  ./test_view  -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
  ./test_view  xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#repeated.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
  ./test_view  xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
  ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
  ./test_view  -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
  ./test_view  xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#repeated2.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam
  ./test_view  xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_
  ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./test_view  -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./test_view  xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#rg.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
  ./test_view  xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
  ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
  ./test_view  -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
  ./test_view  xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#tlen.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
  ./test_view  xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
  ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view  -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
  ./test_view  xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#tlen2.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
  ./test_view  xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
  ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
  ./test_view  -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
  ./test_view  xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#triplet.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
  ./test_view  xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
  ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
  ./test_view  -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
  ./test_view  xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#u.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#u.sam > xx#u.tmp.bam
  ./test_view  xx#u.tmp.bam > xx#u.tmp.bam.sam_
  ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram
  ./test_view  -D xx#u.tmp.cram > xx#u.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram
  ./test_view  xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#unsorted.sam, ref xx.fa:
  ./test_view  -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
  ./test_view  xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
  ./test_view  -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
  ./test_view  -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
  ./test_view  -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
  ./test_view  xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
.. ok

test_view testing BAM records in multiple BGZF blocks:
  ./test_view  -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam
  ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam
  ./test_view  -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam
  ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam
  ./test_view  -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam
  ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam
  ./test_view  -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam
  ./test_view  -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam
  ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam
.. ok

test_view testing embed_ref=2:
  ./test_view  -C -p ce#1000_er.tmp.cram ce#1000.sam
[W::cram_get_ref] Failed to populate reference "CHROMOSOME_I"
[W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions
[W::cram_write_SAM_hdr] No M5 tags present and could not find reference
[W::cram_write_SAM_hdr] Enabling embed_ref=2 option
[W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference
  ./test_view  -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram
  ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam
  ./test_view  -C -p c1#bounds_er.tmp.cram c1#bounds.sam
[W::cram_get_ref] Failed to populate reference "c1"
[W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions
[W::cram_write_SAM_hdr] No M5 tags present and could not find reference
[W::cram_write_SAM_hdr] Enabling embed_ref=2 option
[W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference
  ./test_view  -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram
  ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam
  ./test_view  -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam
  ./test_view  -p embed_MD.tmp.cram.sam embed_MD.tmp.cram
  ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam
.. ok

test_view testing region queries:
  ./test_view  -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view  range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view  -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp
  ./compare_sam.pl range.tmp range.out2
  ./test_view  -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp
  ./compare_sam.pl range.tmp range.out2
.. ok

test_view testing BAM files with absent @SQ lines:
  ./test_view  -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
  ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
  ./test_view  -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
  ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok

test_view testing large (> 2Gbases) positions:
  ./test_view  -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
  ./test_view  -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
  ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok

  ./test_view  -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
  ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
  ./test_view  -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
  ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok

test_view testing auxf#values.sam, ref auxf.fa:
  ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam
  ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_
  ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_
  ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
  ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
  ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
  ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_
.. ok

test_view testing c1#bounds.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam
  ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_
  ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram
  ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
  ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#bounds_er.tmp.cram.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam
  ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_
  ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram
  ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram
  ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#clip.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam
  ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_
  ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram
  ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
  ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#noseq.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam
  ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_
  ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram
  ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
  ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#pad1.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam
  ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_
  ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram
  ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
  ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#pad2.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam
  ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_
  ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram
  ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
  ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
.. ok

test_view testing c1#pad3.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam
  ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_
  ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
  ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram
  ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_
.. ok

test_view testing c1#unknown.sam, ref c1.fa:
  ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam
  ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_
  ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_
  ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram
  ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
  ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
  ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
.. ok

test_view testing c2#pad.sam, ref c2.fa:
  ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam
  ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_
  ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_
  ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram
  ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
  ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
  ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#1.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam
  ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_
  ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram
  ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram
  ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#1000.sam, ref ce.fa:
  ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam
  ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_
  ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram
  ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms
  ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_
.. ok

test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam
  ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_
  ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram
  ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram
  ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#2.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam
  ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_
  ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram
  ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram
  ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#5.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam
  ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_
  ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram
  ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram
  ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms
  ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram
  ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_
.. ok

test_view testing ce#5b.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam
  ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_
  ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram
  ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
  ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms
  ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_
  ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
  ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok

test_view testing ce#large_seq.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam
  ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_
  ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
  ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_
.. ok

test_view testing ce#supp.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam
  ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_
  ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram
  ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
  ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram
  ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_
.. ok

test_view testing ce#tag_depadded.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam
  ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram
  ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
  ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#tag_padded.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam
  ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_
  ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram
  ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
  ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
.. ok

test_view testing ce#unmap.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam
  ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_
  ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram
  ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
  ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms
  ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_
.. ok

test_view testing ce#unmap1.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam
  ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_
  ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram
  ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
  ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms
  ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_
.. ok

test_view testing ce#unmap2.sam, ref ce.fa:
  ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam
  ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_
  ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_
  ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram
  ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
  ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms
  ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_
.. ok

test_view testing md#1.sam, ref md.fa:
  ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam
  ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_
  ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_
  ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram
  ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.cram.sam_
  ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram
  ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_
  ./compare_sam.pl  md#1.sam md#1.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#blank.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam
  ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_
  ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram
  ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
  ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms
  ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram
  ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_
.. ok

test_view testing xx#large_aux.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam
  ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
  ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_
  ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20
  ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_
.. ok

test_view testing xx#large_aux2.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam
  ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_
  ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram
  ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
  ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#MD.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam
  ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_
  ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram
  ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram
  ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram
  ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_
.. ok

test_view testing xx#MD2.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam
  ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram
  ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#minimal.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam
  ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_
  ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram
  ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
  ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms
  ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_
.. ok

test_view testing xx#pair.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam
  ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_
  ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram
  ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
  ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram
  ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_
.. ok

test_view testing xx#repeated.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam
  ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_
  ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram
  ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
  ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#repeated2.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#repeated2.sam > xx#repeated2.tmp.bam
  ./test_view -@4 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.sam_
  ./compare_sam.pl xx#repeated2.sam xx#repeated2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated2.sam > xx#repeated2.tmp.cram
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./test_view -@4 -D xx#repeated2.tmp.cram > xx#repeated2.tmp.cram.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated2.tmp.bam > xx#repeated2.tmp.bam.cram
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./test_view -@4 xx#repeated2.tmp.bam.cram > xx#repeated2.tmp.bam.cram.bam.sam_
[W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 100 vs 20
  ./compare_sam.pl -nomd xx#repeated2.sam xx#repeated2.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#rg.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam
  ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_
  ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram
  ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
  ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#tlen.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam
  ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_
  ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
  ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms
  ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram
  ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram
[W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change.
This is a technology demonstration that should not be used for archival data.
  ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_
.. ok

test_view testing xx#tlen2.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam
  ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_
  ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram
  ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
  ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms
  ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_
.. ok

test_view testing xx#triplet.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam
  ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_
  ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram
  ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
  ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms
  ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_
  ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_
.. ok

test_view testing xx#u.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam
  ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_
  ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram
  ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram
  ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_
.. ok

test_view testing xx#unsorted.sam, ref xx.fa:
  ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam
  ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_
  ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_
  ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram
  ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
  ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
  ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_
  ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
.. ok

test_view testing BAM records in multiple BGZF blocks:
  ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam
  ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam
  ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam
  ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam
  ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam
  ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam
  ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam
  ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam
  ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam
.. ok

test_view testing embed_ref=2:
  ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam
[W::cram_get_ref] Failed to populate reference "CHROMOSOME_I"
[W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions
[W::cram_write_SAM_hdr] No M5 tags present and could not find reference
[W::cram_write_SAM_hdr] Enabling embed_ref=2 option
[W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference
  ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram
  ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam
  ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam
[W::cram_get_ref] Failed to populate reference "c1"
[W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions
[W::cram_write_SAM_hdr] No M5 tags present and could not find reference
[W::cram_write_SAM_hdr] Enabling embed_ref=2 option
[W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference
  ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram
  ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam
  ./test_view -@4 -o embed_ref=2 -o seqs_per_slice=3 -o bases_per_slice=1000000 -C -p embed_MD.tmp.cram embed_MD.sam
  ./test_view -@4 -p embed_MD.tmp.cram.sam embed_MD.tmp.cram
  ./compare_sam.pl embed_MD.sam embed_MD.tmp.cram.sam
.. ok

test_view testing region queries:
  ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp
  ./compare_sam.pl range.tmp range.out
  ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp
  ./compare_sam.pl range.tmp range.out2
  ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp
  ./compare_sam.pl range.tmp range.out2
.. ok

test_view testing BAM files with absent @SQ lines:
  ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam
  ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam
  ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I
  ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam
.. ok

test_view testing large (> 2Gbases) positions:
  ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam
  ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz
  ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_
test_view:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c longrefs/longref.tmp.sam.gz
.. ok

  ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003
  ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam
  ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110
  ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam
.. ok


test_MD testing xx#MD.sam, ref xx.fa:
  ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_
  ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_
  Checking for MD/NM in xx#MD.sam
  ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram
  ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_
  ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_
.. ok


test_MD testing xx#MD2.sam, ref xx.fa:
  ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_
  ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram
  ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_
  ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_
.. ok

test_vcf_api:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-vcf-api /tmp/q3ZAyExF5w/test-vcf-api.bcf
.. ok

test_bcf2vcf:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/tabix/vcf_file.bcf
.. ok

test_vcf_sweep:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-vcf-sweep /tmp/q3ZAyExF5w/test-vcf-api.bcf
.. ok

test_vcf_various:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -ch /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-vcf-hdr-in.vcf
.. ok

test_vcf_various:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/formatcols.vcf
.. ok

test_vcf_various:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/noroundtrip.vcf
.. ok

test_vcf_various:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/formatmissing.vcf
.. ok

test_vcf_various:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/vcf_meta_meta.vcf
.. ok

test_vcf_various:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/modhdr.vcf.gz chr22:1-2
.. ok

test_vcf_44:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile -c /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/vcf44_1.vcf
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 74452500
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 34270147
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 11108528
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 42233895
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 8111117
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 85644070
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 49879942
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 47881429
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 69081244
.. ok

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/q3ZAyExF5w -s 83459376
.. ok

test_bcf_sr_no_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.b.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/q3ZAyExF5w/no_index_1.err
.. ok

test_bcf_sr_no_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/q3ZAyExF5w/no_index_2.out 2> /tmp/q3ZAyExF5w/no_index_2.err (expected fail)
.. ok

test_bcf_sr_no_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/q3ZAyExF5w/no_index_3.out 2> /tmp/q3ZAyExF5w/no_index_3.err (expected fail)
.. ok

test_bcf_sr_no_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr --no-index -p all --args /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.rec_order.vcf /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/merge.noidx.a.vcf > /tmp/q3ZAyExF5w/no_index_4.out 2> /tmp/q3ZAyExF5w/no_index_4.err (expected fail)
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -b -p /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf -x /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bcf-sr/weird-chr-names.vcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_1.out.vcf -r '1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_2.out.vcf -r '1:1-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_4.out.vcf -r '1:1-1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_5.out.vcf -r '{1:1}' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf (expected fail)
[E::_regions_init_string] Could not parse the region(s): {1:1-1}-2
Failed to set regions
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_14.out.vcf -t '1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_15.out.vcf -t '1:1-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_17.out.vcf -t '1:1-1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_18.out.vcf -t '{1:1}' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf
.. ok

test_bcf_sr_range:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr -O vcf -o /tmp/q3ZAyExF5w/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/q3ZAyExF5w/weird-chr-names.vcf.bcf (expected fail)
[E::_regions_init_string] Could not parse the region(s): {1:1-1}-2
Failed to set targets
.. ok

.. ok

test_command:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-translate -
.. ok

test_convert_padded_header:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -t ce.fa -C /tmp/q3ZAyExF5w/headernul0.bam
.. ok

test_convert_padded_header:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -t ce.fa -C /tmp/q3ZAyExF5w/headernul1.bam
.. ok

test_convert_padded_header:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -t ce.fa -C /tmp/q3ZAyExF5w/headernul678.bam
.. ok

test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/bgzip -I /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bgziptest.txt.tmp.gz.gzi -c -g /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/bgziptest.txt
.. ok

test-logging:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-logging.pl
.. ok

test_plugin_loading:
	HTS_PATH=/builddir/build/BUILD/htslib-1.23-build/htslib-1.23 /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/with-shlib.sh /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/htsfile https://localhost:99999/invalid_port
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn01.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -e -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -r -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02-r.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -a -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02_exp.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02.fa -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn02_exp-a.sam -o -
.. ok

test_realn:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_realn -f /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn03.fa -e -i /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/realn03.sam -o -
.. ok

test-bcf_set_variant_type:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf_set_variant_type
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -c chr,beg,end -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl,value:overlap,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl,value:overlap,value -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -O 0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -rO 0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.1.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.1.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.2.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.2.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.3.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.3.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.3.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.3.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.3.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl:overlap -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.3.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.4.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.4.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.4.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.4.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.4.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.4.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.5.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.5.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.5.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.5.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.5.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.5.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.6.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.6.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.6.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.6.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.6.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.6.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.7.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.7.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.7.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.7.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.7.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.7.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.8.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.8.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.8.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.8.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.8.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.8.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.9.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.9.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.9.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.9.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.9.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.9.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -f smpl -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv  -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv  -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv  -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -x -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -f smpl -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -f smpl -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl  -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl  -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl  -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -x -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.10.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -m smpl -x -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.10.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.12.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.12.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.12.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.12.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.11.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.13.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 11:11 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt
.. ok

run_annot_tsv:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -s /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt
.. ok

run_annot_tsv:
	cat /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/src.14.txt | /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/annot-tsv -c 1,2,3 -C 01:01 -t /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/annot-tsv/dst.14.txt
.. ok

ref-cache:
  ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam
  ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram
  ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam
  ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram
  ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam
  ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram
  ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam
.. ok


Number of tests:
    total   .. 358
    passed  .. 358
    failed  .. 0

+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: htslib-1.23-1.fc44.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gWhBp9
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.23-build
+ cd htslib-1.23
+ DOCDIR=/builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/doc/htslib
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/doc/htslib
+ cp -pr /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/NEWS /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/doc/htslib
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Ibzlfl
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.23-build
+ cd htslib-1.23
+ LICENSEDIR=/builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/licenses/htslib
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/licenses/htslib
+ cp -pr /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/LICENSE /builddir/build/BUILD/htslib-1.23-build/BUILDROOT/usr/share/licenses/htslib
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: htslib = 1.23-1.fc44 htslib(x86-64) = 1.23-1.fc44 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_1.13)(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_1.20)(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)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) 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_2.3.2)(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) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) libhts.so.3(HTSLIB_1.0)(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_1.7)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-devel-1.23-1.fc44.x86_64
Provides: htslib-devel = 1.23-1.fc44 htslib-devel(x86-64) = 1.23-1.fc44 pkgconfig(htslib) = 1.23
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config libhts.so.3()(64bit)
Processing files: htslib-tools-1.23-1.fc44.x86_64
Provides: htslib-tools = 1.23-1.fc44 htslib-tools(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: libbz2.so.1()(64bit) 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_2.3.2)(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) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-debugsource-1.23-1.fc44.x86_64
Provides: htslib-debugsource = 1.23-1.fc44 htslib-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: htslib-debuginfo-1.23-1.fc44.x86_64
Provides: debuginfo(build-id) = 7335de7c58891cc4613e59e1f2f9be8360ab1702 debuginfo(build-id) = 7813134e23916bd5214e98af88c4650ccca3a3c5 debuginfo(build-id) = 8b213e742a659aa1f72ff5f092e9aa349e5e21fe debuginfo(build-id) = ce638b8e49fd14a57cbfa006e6719f9e4e2b0350 htslib-debuginfo = 1.23-1.fc44 htslib-debuginfo(x86-64) = 1.23-1.fc44 libhts.so.1.23-1.23-1.fc44.x86_64.debug()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: htslib-debugsource(x86-64) = 1.23-1.fc44
Processing files: htslib-tools-debuginfo-1.23-1.fc44.x86_64
Provides: debuginfo(build-id) = b78ca4c07eb89aa07e059cb3aba7712faa049cdc debuginfo(build-id) = bff8cf222e23f5cc4e7fab7a74f947fd19001933 debuginfo(build-id) = d14136b07ba8983e4fe1d449c68f2fc90cd826af debuginfo(build-id) = ef6cefb6316c3469a203edd8b2eff287e9a06bb1 debuginfo(build-id) = fb1a7f853341a811638489860dedb8883cd6239c htslib-tools-debuginfo = 1.23-1.fc44 htslib-tools-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: htslib-debugsource(x86-64) = 1.23-1.fc44
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/htslib-1.23-build/BUILDROOT
Wrote: /builddir/build/RPMS/htslib-debuginfo-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-debugsource-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-devel-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-tools-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-1.23-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.23-1.fc44.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.3J6VfI
+ umask 022
+ cd /builddir/build/BUILD/htslib-1.23-build
+ test -d /builddir/build/BUILD/htslib-1.23-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/htslib-1.23-build
+ rm -rf /builddir/build/BUILD/htslib-1.23-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild htslib-1.23-1.fc44.src.rpm
Finish: build phase for htslib-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_64-1769500767.470292/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/htslib-1.23-1.fc44.src.rpm) Config(child) 4 minutes 55 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": "htslib-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "htslib-tools",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "htslib-devel",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "htslib-debugsource",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "htslib-tools-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "htslib",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "htslib",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "src"
        }
    ]
}
RPMResults finished