Warning: Permanently added '44.201.226.106' (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/10066849-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64


Version: 1.6
PID: 9591
Logging PID: 9593
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 10066849,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': 'd3435d690e0a26c48268fb334fee5b60542a52d1',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/htslib',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'htslib',
 'package_version': '1.23-1',
 'project_dirname': 'staging',
 'project_name': 'staging',
 'project_owner': 'ron',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ron/staging/fedora-rawhide-aarch64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ron/staging--ron',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'ron',
 'tags': [],
 'task_id': '10066849-fedora-rawhide-aarch64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ron/staging/htslib /var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/htslib --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ron/staging/htslib', '/var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/htslib', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/htslib'...

Running: git checkout d3435d690e0a26c48268fb334fee5b60542a52d1 --

cmd: ['git', 'checkout', 'd3435d690e0a26c48268fb334fee5b60542a52d1', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/htslib
rc: 0
stdout: 
stderr: Note: switching to 'd3435d690e0a26c48268fb334fee5b60542a52d1'.

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 d3435d6 automatic import of htslib

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/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/staging/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   159M      0 --:--:-- --:--:-- --:--:--  161M
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-3cpn7ejv/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769507958.610212 -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-3cpn7ejv/htslib/htslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3cpn7ejv/htslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1769507958.610212 -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-3cpn7ejv/htslib/htslib.spec)  Config(fedora-rawhide-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.6
INFO: Mock Version: 6.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1769507958.610212/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-1347ba5c-dfda-4b48-ac52-77f02dfae218
INFO: Checking that ada545071707428d4e9e51ee4055b80dbe0152a0d651ff91d5a4f1d06af5a8df image matches host's architecture
INFO: Copy content of container ada545071707428d4e9e51ee4055b80dbe0152a0d651ff91d5a4f1d06af5a8df to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1769507958.610212/root
INFO: mounting ada545071707428d4e9e51ee4055b80dbe0152a0d651ff91d5a4f1d06af5a8df with podman image mount
INFO: image ada545071707428d4e9e51ee4055b80dbe0152a0d651ff91d5a4f1d06af5a8df as /var/lib/containers/storage/overlay/0c33bae2a56b903472f969cc6f570bda0d2f4bb373df30b20261dbe4e686575a/merged
INFO: umounting image ada545071707428d4e9e51ee4055b80dbe0152a0d651ff91d5a4f1d06af5a8df (/var/lib/containers/storage/overlay/0c33bae2a56b903472f969cc6f570bda0d2f4bb373df30b20261dbe4e686575a/merged) with podman image umount
INFO: Removing image mock-bootstrap-1347ba5c-dfda-4b48-ac52-77f02dfae218
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-aarch64-1769507958.610212/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.aarch64
  rpm-sequoia-1.10.0-2.fc44.aarch64
  dnf5-5.3.0.0-7.fc44.aarch64
  dnf5-plugins-5.3.0.0-7.fc44.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  10.9 MiB/s |  21.0 MiB |  00m02s
 Copr repository                        100% | 900.0   B/s |   1.6 KiB |  00m02s
Repositories loaded.
Package                            Arch    Version                      Repository      Size
Installing group/module packages:
 bash                              aarch64 0:5.3.9-3.fc44               fedora       8.4 MiB
 bzip2                             aarch64 0:1.0.8-23.fc44              fedora     171.1 KiB
 coreutils                         aarch64 0:9.9-4.fc44                 fedora       8.1 MiB
 cpio                              aarch64 0:2.15-6.fc43                fedora       1.1 MiB
 diffutils                         aarch64 0:3.12-5.fc44                fedora       1.6 MiB
 fedora-release-common             noarch  0:44-0.10                    fedora      20.6 KiB
 findutils                         aarch64 1:4.10.0-7.fc44              fedora       1.9 MiB
 gawk                              aarch64 0:5.3.2-3.fc44               fedora       2.6 MiB
 glibc-minimal-langpack            aarch64 0:2.42.9000-25.fc44          fedora       0.0   B
 grep                              aarch64 0:3.12-3.fc44                fedora       1.0 MiB
 gzip                              aarch64 0:1.14-2.fc44                fedora     437.5 KiB
 info                              aarch64 0:7.2-7.fc44                 fedora     421.6 KiB
 patch                             aarch64 0:2.8-4.fc44                 fedora     262.4 KiB
 redhat-rpm-config                 noarch  0:343-19.fc44                fedora     183.6 KiB
 rpm-build                         aarch64 0:6.0.1-2.fc44               fedora     598.3 KiB
 sed                               aarch64 0:4.9-7.fc44                 fedora     873.1 KiB
 shadow-utils                      aarch64 2:4.18.0-7.fc44              fedora       4.4 MiB
 tar                               aarch64 2:1.35-8.fc44                fedora       3.0 MiB
 unzip                             aarch64 0:6.0-69.fc44                fedora     533.8 KiB
 util-linux                        aarch64 0:2.41.3-12.fc44             fedora       6.8 MiB
 which                             aarch64 0:2.23-4.fc44                fedora     123.3 KiB
 xz                                aarch64 1:5.8.2-2.fc44               fedora       1.4 MiB
Installing dependencies:
 R-srpm-macros                     noarch  0:1.3.4-3.fc44               fedora       3.4 KiB
 add-determinism                   aarch64 0:0.7.2-3.fc44               fedora       2.0 MiB
 alternatives                      aarch64 0:1.33-5.fc44                fedora      90.1 KiB
 ansible-srpm-macros               noarch  0:1-20.1.fc44                fedora      35.7 KiB
 audit-libs                        aarch64 0:4.1.2-4.fc44               fedora     486.5 KiB
 binutils                          aarch64 0:2.45.50-19.fc44            fedora      30.7 MiB
 build-reproducibility-srpm-macros noarch  0:0.7.2-3.fc44               fedora       1.2 KiB
 bzip2-libs                        aarch64 0:1.0.8-23.fc44              fedora      72.5 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                  aarch64 0:9.9-4.fc44                 fedora      11.2 MiB
 crypto-policies                   noarch  0:20251128-3.git19878fe.fc44 fedora     132.6 KiB
 curl                              aarch64 0:8.18.0-3.fc44              fedora     464.1 KiB
 cyrus-sasl-lib                    aarch64 0:2.1.28-35.fc44             fedora       2.4 MiB
 debugedit                         aarch64 0:5.2-6.fc44                 fedora     318.3 KiB
 dwz                               aarch64 0:0.16-3.fc44                fedora     322.4 KiB
 ed                                aarch64 0:1.22.4-2.fc44              fedora     157.1 KiB
 efi-srpm-macros                   noarch  0:6-6.fc44                   fedora      40.2 KiB
 elfutils                          aarch64 0:0.194-3.fc44               fedora       3.3 MiB
 elfutils-debuginfod-client        aarch64 0:0.194-3.fc44               fedora     143.7 KiB
 elfutils-default-yama-scope       noarch  0:0.194-3.fc44               fedora       1.8 KiB
 elfutils-libelf                   aarch64 0:0.194-3.fc44               fedora       1.1 MiB
 elfutils-libs                     aarch64 0:0.194-3.fc44               fedora     746.4 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                              aarch64 0:5.46-9.fc44                fedora     140.1 KiB
 file-libs                         aarch64 0:5.46-9.fc44                fedora      11.9 MiB
 filesystem                        aarch64 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                       aarch64 0:17.1-2.fc44                fedora      13.7 MiB
 gdbm-libs                         aarch64 1:1.23-11.fc44               fedora     233.7 KiB
 ghc-srpm-macros                   noarch  0:1.9.2-4.fc44               fedora     779.0   B
 glibc                             aarch64 0:2.42.9000-25.fc44          fedora       6.4 MiB
 glibc-common                      aarch64 0:2.42.9000-25.fc44          fedora       1.3 MiB
 glibc-gconv-extra                 aarch64 0:2.42.9000-25.fc44          fedora      18.5 MiB
 gmp                               aarch64 1:6.3.0-5.fc44               fedora     657.9 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                            aarch64 0:2.4.9-4.fc44               fedora       6.4 MiB
 gnupg2-dirmngr                    aarch64 0:2.4.9-4.fc44               fedora     646.1 KiB
 gnupg2-gpg-agent                  aarch64 0:2.4.9-4.fc44               fedora     846.6 KiB
 gnupg2-gpgconf                    aarch64 0:2.4.9-4.fc44               fedora     321.7 KiB
 gnupg2-keyboxd                    aarch64 0:2.4.9-4.fc44               fedora     233.2 KiB
 gnupg2-verify                     aarch64 0:2.4.9-4.fc44               fedora     364.3 KiB
 gnutls                            aarch64 0:3.8.11-10.fc44             fedora       3.6 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                aarch64 0:1.6.2-8.fc44               fedora      92.6 KiB
 jansson                           aarch64 0:2.14-4.fc44                fedora      93.0 KiB
 java-srpm-macros                  noarch  0:1-8.fc44                   fedora     870.0   B
 json-c                            aarch64 0:0.18-8.fc44                fedora     138.5 KiB
 kernel-srpm-macros                noarch  0:1.0-28.fc44                fedora       1.9 KiB
 keyutils-libs                     aarch64 0:1.6.3-7.fc44               fedora      98.2 KiB
 krb5-libs                         aarch64 0:1.21.3-12.fc44             fedora       2.5 MiB
 libacl                            aarch64 0:2.3.2-6.fc44               fedora      67.8 KiB
 libarchive                        aarch64 0:3.8.4-2.fc44               fedora     975.1 KiB
 libassuan                         aarch64 0:2.5.7-5.fc44               fedora     215.8 KiB
 libattr                           aarch64 0:2.5.2-8.fc44               fedora      68.3 KiB
 libblkid                          aarch64 0:2.41.3-12.fc44             fedora     290.3 KiB
 libbrotli                         aarch64 0:1.2.0-3.fc44               fedora     909.1 KiB
 libcap                            aarch64 0:2.77-2.fc44                fedora     508.0 KiB
 libcap-ng                         aarch64 0:0.9-5.fc44                 fedora     160.7 KiB
 libcom_err                        aarch64 0:1.47.3-4.fc44              fedora     111.0 KiB
 libcurl                           aarch64 0:8.18.0-3.fc44              fedora     980.9 KiB
 libeconf                          aarch64 0:0.7.9-3.fc44               fedora      80.8 KiB
 libevent                          aarch64 0:2.1.12-17.fc44             fedora       1.1 MiB
 libfdisk                          aarch64 0:2.41.3-12.fc44             fedora     418.7 KiB
 libffi                            aarch64 0:3.5.2-2.fc44               fedora     155.7 KiB
 libfsverity                       aarch64 0:1.6-4.fc44                 fedora      68.4 KiB
 libgcc                            aarch64 0:16.0.1-0.3.fc44.1          fedora     222.2 KiB
 libgcrypt                         aarch64 0:1.11.2-1.fc44              fedora       1.2 MiB
 libgomp                           aarch64 0:16.0.1-0.3.fc44.1          fedora     590.9 KiB
 libgpg-error                      aarch64 0:1.58-2.fc44                fedora     989.6 KiB
 libidn2                           aarch64 0:2.3.8-3.fc44               fedora     560.4 KiB
 libksba                           aarch64 0:1.6.7-5.fc44               fedora     398.3 KiB
 liblastlog2                       aarch64 0:2.41.3-12.fc44             fedora     137.7 KiB
 libmount                          aarch64 0:2.41.3-12.fc44             fedora     420.0 KiB
 libnghttp2                        aarch64 0:1.68.0-3.fc44              fedora     197.9 KiB
 libnghttp3                        aarch64 0:1.15.0-1.fc44              fedora     206.6 KiB
 libpkgconf                        aarch64 0:2.3.0-4.fc44               fedora     133.9 KiB
 libpsl                            aarch64 0:0.21.5-7.fc44              fedora     132.3 KiB
 libselinux                        aarch64 0:3.9-7.fc44                 fedora     201.0 KiB
 libselinux-utils                  aarch64 0:3.9-7.fc44                 fedora       1.3 MiB
 libsemanage                       aarch64 0:3.9-5.fc44                 fedora     359.9 KiB
 libsepol                          aarch64 0:3.9-3.fc44                 fedora     809.6 KiB
 libsmartcols                      aarch64 0:2.41.3-12.fc44             fedora     224.4 KiB
 libssh                            aarch64 0:0.11.3-1.fc44              fedora     587.0 KiB
 libssh-config                     noarch  0:0.11.3-1.fc44              fedora     277.0   B
 libstdc++                         aarch64 0:16.0.1-0.3.fc44.1          fedora       2.8 MiB
 libtasn1                          aarch64 0:4.20.0-3.fc44              fedora     220.2 KiB
 libtool-ltdl                      aarch64 0:2.5.4-10.fc44              fedora      93.9 KiB
 libunistring                      aarch64 0:1.1-11.fc44                fedora       1.7 MiB
 libusb1                           aarch64 0:1.0.29-5.fc44              fedora     178.8 KiB
 libuuid                           aarch64 0:2.41.3-12.fc44             fedora      69.3 KiB
 libverto                          aarch64 0:0.3.2-12.fc44              fedora      69.3 KiB
 libxcrypt                         aarch64 0:4.5.2-3.fc44               fedora     273.2 KiB
 libxml2                           aarch64 0:2.12.10-6.fc44             fedora       1.9 MiB
 libzstd                           aarch64 0:1.5.7-5.fc44               fedora     860.2 KiB
 linkdupes                         aarch64 0:0.7.2-3.fc44               fedora     779.1 KiB
 lua-libs                          aarch64 0:5.4.8-5.fc44               fedora     329.8 KiB
 lua-srpm-macros                   noarch  0:1-17.fc44                  fedora       1.3 KiB
 lz4-libs                          aarch64 0:1.10.0-4.fc44              fedora     197.3 KiB
 mpfr                              aarch64 0:4.2.2-3.fc44               fedora     755.4 KiB
 ncurses-base                      noarch  0:6.5-9.20250614.fc44        fedora     328.1 KiB
 ncurses-libs                      aarch64 0:6.5-9.20250614.fc44        fedora       1.2 MiB
 nettle                            aarch64 0:3.10.1-3.fc44              fedora     765.0 KiB
 ngtcp2                            aarch64 0:1.19.0-2.fc44              fedora     341.0 KiB
 ngtcp2-crypto-ossl                aarch64 0:1.19.0-2.fc44              fedora      67.4 KiB
 npth                              aarch64 0:1.8-4.fc44                 fedora      93.3 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                          aarch64 0:2.6.10-7.fc44              fedora     761.6 KiB
 openssl-libs                      aarch64 1:3.5.4-2.fc44               fedora       7.4 MiB
 p11-kit                           aarch64 0:0.25.8-2.fc44              fedora       2.5 MiB
 p11-kit-trust                     aarch64 0:0.25.8-2.fc44              fedora     530.0 KiB
 package-notes-srpm-macros         noarch  0:0.5-15.fc44                fedora       1.6 KiB
 pam-libs                          aarch64 0:1.7.2-1.fc44               fedora     222.6 KiB
 pcre2                             aarch64 0:10.47-1.fc44.1             fedora     714.3 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                           aarch64 0:2.3.0-4.fc44               fedora     112.3 KiB
 pkgconf-m4                        noarch  0:2.3.0-4.fc44               fedora      14.4 KiB
 pkgconf-pkg-config                aarch64 0:2.3.0-4.fc44               fedora     990.0   B
 policycoreutils                   aarch64 0:3.9-8.fc44                 fedora       1.5 MiB
 popt                              aarch64 0:1.19-10.fc44               fedora     144.6 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                          aarch64 0:8.3-4.fc44                 fedora     563.5 KiB
 rpm                               aarch64 0:6.0.1-2.fc44               fedora       3.3 MiB
 rpm-build-libs                    aarch64 0:6.0.1-2.fc44               fedora     264.0 KiB
 rpm-libs                          aarch64 0:6.0.1-2.fc44               fedora     995.0 KiB
 rpm-plugin-selinux                aarch64 0:6.0.1-2.fc44               fedora      67.9 KiB
 rpm-sequoia                       aarch64 0:1.10.0-2.fc44              fedora       2.3 MiB
 rpm-sign-libs                     aarch64 0:6.0.1-2.fc44               fedora      67.6 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                       aarch64 0:3.51.2-1.fc44              fedora       1.6 MiB
 systemd-libs                      aarch64 0:259-9.fc44                 fedora       2.5 MiB
 systemd-standalone-sysusers       aarch64 0:259-9.fc44                 fedora     329.5 KiB
 tpm2-tss                          aarch64 0:4.1.3-9.fc44               fedora       2.1 MiB
 tree-sitter-srpm-macros           noarch  0:0.4.2-2.fc44               fedora       8.3 KiB
 util-linux-core                   aarch64 0:2.41.3-12.fc44             fedora       2.4 MiB
 xxhash-libs                       aarch64 0:0.8.3-4.fc44               fedora      85.8 KiB
 xz-libs                           aarch64 1:5.8.2-2.fc44               fedora     265.4 KiB
 zig-srpm-macros                   noarch  0:1-8.fc44                   fedora       1.3 KiB
 zip                               aarch64 0:3.0-45.fc44                fedora     762.0 KiB
 zlib-ng-compat                    aarch64 0:2.3.2-3.fc44               fedora     133.4 KiB
 zstd                              aarch64 0:1.5.7-5.fc44               fedora     562.2 KiB
Installing groups:
 Buildsystem building group                                                                 

Transaction Summary:
 Installing:       182 packages

Total size of inbound packages is 66 MiB. Need to download 66 MiB.
After this operation, 248 MiB extra will be used (install 248 MiB, remove 0 B).
[  1/182] coreutils-0:9.9-4.fc44.aarch6 100% |  15.6 MiB/s |   1.1 MiB |  00m00s
[  2/182] bzip2-0:1.0.8-23.fc44.aarch64 100% | 720.2 KiB/s |  51.9 KiB |  00m00s
[  3/182] bash-0:5.3.9-3.fc44.aarch64   100% |  12.5 MiB/s |   1.8 MiB |  00m00s
[  4/182] fedora-release-common-0:44-0. 100% |   3.4 MiB/s |  24.7 KiB |  00m00s
[  5/182] diffutils-0:3.12-5.fc44.aarch 100% |   1.2 MiB/s | 391.9 KiB |  00m00s
[  6/182] findutils-1:4.10.0-7.fc44.aar 100% |   1.0 MiB/s | 552.0 KiB |  00m01s
[  7/182] glibc-minimal-langpack-0:2.42 100% |  10.7 MiB/s |  76.9 KiB |  00m00s
[  8/182] cpio-0:2.15-6.fc43.aarch64    100% | 365.2 KiB/s | 289.6 KiB |  00m01s
[  9/182] gzip-0:1.14-2.fc44.aarch64    100% |  14.1 MiB/s | 172.8 KiB |  00m00s
[ 10/182] gawk-0:5.3.2-3.fc44.aarch64   100% |   2.0 MiB/s |   1.1 MiB |  00m01s
[ 11/182] patch-0:2.8-4.fc44.aarch64    100% | 419.2 KiB/s | 111.1 KiB |  00m00s
[ 12/182] grep-0:3.12-3.fc44.aarch64    100% | 590.2 KiB/s | 296.3 KiB |  00m01s
[ 13/182] redhat-rpm-config-0:343-19.fc 100% | 749.4 KiB/s |  79.4 KiB |  00m00s
[ 14/182] sed-0:4.9-7.fc44.aarch64      100% |  34.2 MiB/s | 314.8 KiB |  00m00s
[ 15/182] rpm-build-0:6.0.1-2.fc44.aarc 100% | 892.2 KiB/s | 132.0 KiB |  00m00s
[ 16/182] info-0:7.2-7.fc44.aarch64     100% | 352.7 KiB/s | 179.5 KiB |  00m01s
[ 17/182] shadow-utils-2:4.18.0-7.fc44. 100% |  15.8 MiB/s |   1.3 MiB |  00m00s
[ 18/182] unzip-0:6.0-69.fc44.aarch64   100% |   1.7 MiB/s | 200.9 KiB |  00m00s
[ 19/182] util-linux-0:2.41.3-12.fc44.a 100% |   5.5 MiB/s |   1.2 MiB |  00m00s
[ 20/182] tar-2:1.35-8.fc44.aarch64     100% |   2.9 MiB/s | 854.9 KiB |  00m00s
[ 21/182] which-0:2.23-4.fc44.aarch64   100% | 314.8 KiB/s |  41.6 KiB |  00m00s
[ 22/182] filesystem-0:3.18-52.fc44.aar 100% |  83.4 MiB/s |   1.3 MiB |  00m00s
[ 23/182] ncurses-libs-0:6.5-9.20250614 100% |   4.3 MiB/s | 323.8 KiB |  00m00s
[ 24/182] bzip2-libs-0:1.0.8-23.fc44.aa 100% |   5.8 MiB/s |  41.2 KiB |  00m00s
[ 25/182] coreutils-common-0:9.9-4.fc44 100% |  18.8 MiB/s |   2.1 MiB |  00m00s
[ 26/182] xz-1:5.8.2-2.fc44.aarch64     100% |   2.6 MiB/s | 606.6 KiB |  00m00s
[ 27/182] libacl-0:2.3.2-6.fc44.aarch64 100% |   2.9 MiB/s |  24.0 KiB |  00m00s
[ 28/182] libattr-0:2.5.2-8.fc44.aarch6 100% |   2.5 MiB/s |  17.8 KiB |  00m00s
[ 29/182] libcap-0:2.77-2.fc44.aarch64  100% |  12.3 MiB/s |  87.8 KiB |  00m00s
[ 30/182] libselinux-0:3.9-7.fc44.aarch 100% |  10.6 MiB/s |  97.4 KiB |  00m00s
[ 31/182] gmp-1:6.3.0-5.fc44.aarch64    100% |   3.2 MiB/s | 271.0 KiB |  00m00s
[ 32/182] glibc-0:2.42.9000-25.fc44.aar 100% |   4.4 MiB/s |   1.9 MiB |  00m00s
[ 33/182] openssl-libs-1:3.5.4-2.fc44.a 100% |  11.9 MiB/s |   2.5 MiB |  00m00s
[ 34/182] systemd-libs-0:259-9.fc44.aar 100% |   4.9 MiB/s | 789.4 KiB |  00m00s
[ 35/182] fedora-repos-0:44-0.1.noarch  100% |   1.1 MiB/s |   9.1 KiB |  00m00s
[ 36/182] mpfr-0:4.2.2-3.fc44.aarch64   100% |  26.0 MiB/s | 320.0 KiB |  00m00s
[ 37/182] readline-0:8.3-4.fc44.aarch64 100% |  16.6 MiB/s | 221.1 KiB |  00m00s
[ 38/182] glibc-common-0:2.42.9000-25.f 100% |  31.2 MiB/s | 351.3 KiB |  00m00s
[ 39/182] R-srpm-macros-0:1.3.4-3.fc44. 100% | 983.6 KiB/s |  10.8 KiB |  00m00s
[ 40/182] pcre2-0:10.47-1.fc44.1.aarch6 100% |  13.6 MiB/s | 250.2 KiB |  00m00s
[ 41/182] ansible-srpm-macros-0:1-20.1. 100% |   2.0 MiB/s |  20.1 KiB |  00m00s
[ 42/182] build-reproducibility-srpm-ma 100% |   1.8 MiB/s |  13.0 KiB |  00m00s
[ 43/182] ed-0:1.22.4-2.fc44.aarch64    100% |   3.1 MiB/s |  83.6 KiB |  00m00s
[ 44/182] cmake-srpm-macros-0:3.31.10-5 100% |   1.3 MiB/s |  10.6 KiB |  00m00s
[ 45/182] efi-srpm-macros-0:6-6.fc44.no 100% |   2.8 MiB/s |  22.6 KiB |  00m00s
[ 46/182] filesystem-srpm-macros-0:3.18 100% |   3.3 MiB/s |  26.6 KiB |  00m00s
[ 47/182] fonts-srpm-macros-1:5.0.0-2.f 100% |   3.8 MiB/s |  27.4 KiB |  00m00s
[ 48/182] dwz-0:0.16-3.fc44.aarch64     100% |   4.1 MiB/s | 131.3 KiB |  00m00s
[ 49/182] forge-srpm-macros-0:0.4.0-4.f 100% |   2.4 MiB/s |  20.0 KiB |  00m00s
[ 50/182] fpc-srpm-macros-0:1.3-16.fc44 100% | 992.3 KiB/s |   7.9 KiB |  00m00s
[ 51/182] gap-srpm-macros-0:2-2.fc44.no 100% |   1.3 MiB/s |   9.1 KiB |  00m00s
[ 52/182] file-0:5.46-9.fc44.aarch64    100% |   1.4 MiB/s |  49.1 KiB |  00m00s
[ 53/182] ghc-srpm-macros-0:1.9.2-4.fc4 100% |   1.2 MiB/s |   8.9 KiB |  00m00s
[ 54/182] gnat-srpm-macros-0:7-2.fc44.n 100% |   1.2 MiB/s |   8.7 KiB |  00m00s
[ 55/182] go-srpm-macros-0:3.8.0-2.fc44 100% |   3.9 MiB/s |  28.2 KiB |  00m00s
[ 56/182] java-srpm-macros-0:1-8.fc44.n 100% |   1.1 MiB/s |   8.1 KiB |  00m00s
[ 57/182] kernel-srpm-macros-0:1.0-28.f 100% |   1.3 MiB/s |   9.0 KiB |  00m00s
[ 58/182] lua-srpm-macros-0:1-17.fc44.n 100% |   1.2 MiB/s |   8.9 KiB |  00m00s
[ 59/182] ocaml-srpm-macros-0:11-3.fc44 100% |   1.3 MiB/s |   9.3 KiB |  00m00s
[ 60/182] openblas-srpm-macros-0:2-21.f 100% |   1.1 MiB/s |   7.8 KiB |  00m00s
[ 61/182] package-notes-srpm-macros-0:0 100% |   1.3 MiB/s |   9.2 KiB |  00m00s
[ 62/182] perl-srpm-macros-0:1-61.fc44. 100% |   1.2 MiB/s |   8.4 KiB |  00m00s
[ 63/182] pyproject-srpm-macros-0:1.18. 100% |   1.9 MiB/s |  13.5 KiB |  00m00s
[ 64/182] python-srpm-macros-0:3.14-10. 100% |   3.3 MiB/s |  24.0 KiB |  00m00s
[ 65/182] qt5-srpm-macros-0:5.15.18-2.f 100% |   1.2 MiB/s |   8.7 KiB |  00m00s
[ 66/182] qt6-srpm-macros-0:6.10.1-2.fc 100% |   1.3 MiB/s |   9.2 KiB |  00m00s
[ 67/182] rpm-0:6.0.1-2.fc44.aarch64    100% |  51.3 MiB/s | 577.8 KiB |  00m00s
[ 68/182] rust-srpm-macros-0:28.4-3.fc4 100% |   1.4 MiB/s |  11.1 KiB |  00m00s
[ 69/182] tree-sitter-srpm-macros-0:0.4 100% |   1.9 MiB/s |  13.5 KiB |  00m00s
[ 70/182] zig-srpm-macros-0:1-8.fc44.no 100% |   1.2 MiB/s |   8.8 KiB |  00m00s
[ 71/182] debugedit-0:5.2-6.fc44.aarch6 100% |   3.0 MiB/s |  84.7 KiB |  00m00s
[ 72/182] zip-0:3.0-45.fc44.aarch64     100% |   5.0 MiB/s | 265.6 KiB |  00m00s
[ 73/182] elfutils-libelf-0:0.194-3.fc4 100% |  21.9 MiB/s | 202.3 KiB |  00m00s
[ 74/182] libarchive-0:3.8.4-2.fc44.aar 100% |  27.0 MiB/s | 414.7 KiB |  00m00s
[ 75/182] libgcc-0:16.0.1-0.3.fc44.1.aa 100% |  10.5 MiB/s |  96.5 KiB |  00m00s
[ 76/182] elfutils-0:0.194-3.fc44.aarch 100% |   8.2 MiB/s | 538.6 KiB |  00m00s
[ 77/182] libstdc++-0:16.0.1-0.3.fc44.1 100% |  51.3 MiB/s | 840.3 KiB |  00m00s
[ 78/182] popt-0:1.19-10.fc44.aarch64   100% |   6.4 MiB/s |  65.2 KiB |  00m00s
[ 79/182] rpm-build-libs-0:6.0.1-2.fc44 100% |  16.4 MiB/s | 117.3 KiB |  00m00s
[ 80/182] pkgconf-pkg-config-0:2.3.0-4. 100% | 388.1 KiB/s |   9.7 KiB |  00m00s
[ 81/182] rpm-libs-0:6.0.1-2.fc44.aarch 100% |  36.9 MiB/s | 378.2 KiB |  00m00s
[ 82/182] zstd-0:1.5.7-5.fc44.aarch64   100% |  12.8 MiB/s | 183.1 KiB |  00m00s
[ 83/182] audit-libs-0:4.1.2-4.fc44.aar 100% |  17.2 MiB/s | 141.2 KiB |  00m00s
[ 84/182] libeconf-0:0.7.9-3.fc44.aarch 100% |   4.9 MiB/s |  35.0 KiB |  00m00s
[ 85/182] binutils-0:2.45.50-19.fc44.aa 100% |  39.2 MiB/s |   6.3 MiB |  00m00s
[ 86/182] pam-libs-0:1.7.2-1.fc44.aarch 100% |   7.9 MiB/s |  56.8 KiB |  00m00s
[ 87/182] setup-0:2.15.0-28.fc44.noarch 100% |  21.9 MiB/s | 157.2 KiB |  00m00s
[ 88/182] libsemanage-0:3.9-5.fc44.aarc 100% |   2.1 MiB/s | 118.5 KiB |  00m00s
[ 89/182] libcap-ng-0:0.9-5.fc44.aarch6 100% |   4.6 MiB/s |  32.7 KiB |  00m00s
[ 90/182] libblkid-0:2.41.3-12.fc44.aar 100% |   3.0 MiB/s | 121.8 KiB |  00m00s
[ 91/182] liblastlog2-0:2.41.3-12.fc44. 100% | 567.4 KiB/s |  23.3 KiB |  00m00s
[ 92/182] libxcrypt-0:4.5.2-3.fc44.aarc 100% | 828.7 KiB/s | 125.1 KiB |  00m00s
[ 93/182] libfdisk-0:2.41.3-12.fc44.aar 100% |   1.2 MiB/s | 154.4 KiB |  00m00s
[ 94/182] libsmartcols-0:2.41.3-12.fc44 100% |   1.4 MiB/s |  82.7 KiB |  00m00s
[ 95/182] libuuid-0:2.41.3-12.fc44.aarc 100% | 601.7 KiB/s |  25.9 KiB |  00m00s
[ 96/182] libmount-0:2.41.3-12.fc44.aar 100% |   1.3 MiB/s | 157.8 KiB |  00m00s
[ 97/182] zlib-ng-compat-0:2.3.2-3.fc44 100% |  10.3 MiB/s |  73.7 KiB |  00m00s
[ 98/182] xz-libs-1:5.8.2-2.fc44.aarch6 100% |  15.6 MiB/s | 111.7 KiB |  00m00s
[ 99/182] ncurses-base-0:6.5-9.20250614 100% |  12.3 MiB/s |  88.2 KiB |  00m00s
[100/182] gnulib-l10n-0:20241231-2.fc44 100% |  18.4 MiB/s | 150.3 KiB |  00m00s
[101/182] libsepol-0:3.9-3.fc44.aarch64 100% |   3.7 MiB/s | 324.6 KiB |  00m00s
[102/182] ca-certificates-0:2025.2.80_v 100% |  79.2 MiB/s | 973.5 KiB |  00m00s
[103/182] crypto-policies-0:20251128-3. 100% |  12.0 MiB/s |  98.3 KiB |  00m00s
[104/182] fedora-gpg-keys-0:44-0.1.noar 100% |  15.1 MiB/s | 138.8 KiB |  00m00s
[105/182] fedora-repos-rawhide-0:44-0.1 100% |   1.2 MiB/s |   8.6 KiB |  00m00s
[106/182] util-linux-core-0:2.41.3-12.f 100% |   3.0 MiB/s | 540.2 KiB |  00m00s
[107/182] pcre2-syntax-0:10.47-1.fc44.1 100% |  20.1 MiB/s | 164.7 KiB |  00m00s
[108/182] glibc-gconv-extra-0:2.42.9000 100% |   8.5 MiB/s |   1.7 MiB |  00m00s
[109/182] linkdupes-0:0.7.2-3.fc44.aarc 100% |   3.4 MiB/s | 337.2 KiB |  00m00s
[110/182] curl-0:8.18.0-3.fc44.aarch64  100% |  25.6 MiB/s | 235.6 KiB |  00m00s
[111/182] alternatives-0:1.33-5.fc44.aa 100% |   5.6 MiB/s |  40.4 KiB |  00m00s
[112/182] elfutils-debuginfod-client-0: 100% |   1.1 MiB/s |  45.8 KiB |  00m00s
[113/182] add-determinism-0:0.7.2-3.fc4 100% |   3.9 MiB/s | 823.2 KiB |  00m00s
[114/182] file-libs-0:5.46-9.fc44.aarch 100% |   5.1 MiB/s | 847.9 KiB |  00m00s
[115/182] jansson-0:2.14-4.fc44.aarch64 100% | 397.4 KiB/s |  46.5 KiB |  00m00s
[116/182] libzstd-0:1.5.7-5.fc44.aarch6 100% |   5.2 MiB/s | 329.2 KiB |  00m00s
[117/182] lz4-libs-0:1.10.0-4.fc44.aarc 100% |  10.7 MiB/s |  76.6 KiB |  00m00s
[118/182] libxml2-0:2.12.10-6.fc44.aarc 100% |  60.5 MiB/s | 682.0 KiB |  00m00s
[119/182] pkgconf-m4-0:2.3.0-4.fc44.noa 100% |   2.0 MiB/s |  14.1 KiB |  00m00s
[120/182] pkgconf-0:2.3.0-4.fc44.aarch6 100% |   1.4 MiB/s |  44.5 KiB |  00m00s
[121/182] lua-libs-0:5.4.8-5.fc44.aarch 100% |  15.8 MiB/s | 129.4 KiB |  00m00s
[122/182] rpm-sign-libs-0:6.0.1-2.fc44. 100% |   3.8 MiB/s |  27.1 KiB |  00m00s
[123/182] rpm-sequoia-0:1.10.0-2.fc44.a 100% |  15.7 MiB/s | 885.7 KiB |  00m00s
[124/182] sqlite-libs-0:3.51.2-1.fc44.a 100% |  48.9 MiB/s | 750.9 KiB |  00m00s
[125/182] libffi-0:3.5.2-2.fc44.aarch64 100% |   5.5 MiB/s |  39.6 KiB |  00m00s
[126/182] p11-kit-0:0.25.8-2.fc44.aarch 100% |  36.9 MiB/s | 490.6 KiB |  00m00s
[127/182] elfutils-libs-0:0.194-3.fc44. 100% |   1.2 MiB/s | 263.0 KiB |  00m00s
[128/182] p11-kit-trust-0:0.25.8-2.fc44 100% |  16.9 MiB/s | 138.1 KiB |  00m00s
[129/182] json-c-0:0.18-8.fc44.aarch64  100% |   6.3 MiB/s |  44.9 KiB |  00m00s
[130/182] elfutils-default-yama-scope-0 100% |   1.7 MiB/s |  11.9 KiB |  00m00s
[131/182] libpkgconf-0:2.3.0-4.fc44.aar 100% |   2.1 MiB/s |  37.9 KiB |  00m00s
[132/182] ima-evm-utils-libs-0:1.6.2-8. 100% | 775.4 KiB/s |  29.5 KiB |  00m00s
[133/182] libgomp-0:16.0.1-0.3.fc44.1.a 100% |   1.6 MiB/s | 357.0 KiB |  00m00s
[134/182] libfsverity-0:1.6-4.fc44.aarc 100% | 435.8 KiB/s |  18.7 KiB |  00m00s
[135/182] gpgverify-0:2.2-4.fc44.noarch 100% |   1.6 MiB/s |  11.2 KiB |  00m00s
[136/182] gnupg2-0:2.4.9-4.fc44.aarch64 100% |  12.5 MiB/s |   1.6 MiB |  00m00s
[137/182] libtasn1-0:4.20.0-3.fc44.aarc 100% | 843.6 KiB/s |  73.4 KiB |  00m00s
[138/182] gnupg2-dirmngr-0:2.4.9-4.fc44 100% |   4.2 MiB/s | 264.2 KiB |  00m00s
[139/182] gnupg2-gpgconf-0:2.4.9-4.fc44 100% |   5.1 MiB/s | 113.9 KiB |  00m00s
[140/182] gnupg2-keyboxd-0:2.4.9-4.fc44 100% |   1.8 MiB/s |  91.3 KiB |  00m00s
[141/182] gnupg2-gpg-agent-0:2.4.9-4.fc 100% |   2.1 MiB/s | 265.8 KiB |  00m00s
[142/182] libassuan-0:2.5.7-5.fc44.aarc 100% |   1.3 MiB/s |  66.9 KiB |  00m00s
[143/182] gnupg2-verify-0:2.4.9-4.fc44. 100% |   1.5 MiB/s | 163.5 KiB |  00m00s
[144/182] npth-0:1.8-4.fc44.aarch64     100% | 626.2 KiB/s |  25.0 KiB |  00m00s
[145/182] libgpg-error-0:1.58-2.fc44.aa 100% |   3.8 MiB/s | 248.3 KiB |  00m00s
[146/182] gnutls-0:3.8.11-10.fc44.aarch 100% |  67.3 MiB/s |   1.3 MiB |  00m00s
[147/182] libksba-0:1.6.7-5.fc44.aarch6 100% |   1.3 MiB/s | 157.8 KiB |  00m00s
[148/182] libgcrypt-0:1.11.2-1.fc44.aar 100% |   2.3 MiB/s | 519.6 KiB |  00m00s
[149/182] libusb1-0:1.0.29-5.fc44.aarch 100% |   1.9 MiB/s |  78.0 KiB |  00m00s
[150/182] tpm2-tss-0:4.1.3-9.fc44.aarch 100% |   1.5 MiB/s | 401.2 KiB |  00m00s
[151/182] libidn2-0:2.3.8-3.fc44.aarch6 100% |   2.0 MiB/s | 174.6 KiB |  00m00s
[152/182] openldap-0:2.6.10-7.fc44.aarc 100% |   1.1 MiB/s | 251.4 KiB |  00m00s
[153/182] libunistring-0:1.1-11.fc44.aa 100% |   3.9 MiB/s | 538.3 KiB |  00m00s
[154/182] nettle-0:3.10.1-3.fc44.aarch6 100% |   2.5 MiB/s | 425.5 KiB |  00m00s
[155/182] libtool-ltdl-0:2.5.4-10.fc44. 100% |   3.5 MiB/s |  35.6 KiB |  00m00s
[156/182] libevent-0:2.1.12-17.fc44.aar 100% |   4.3 MiB/s | 270.5 KiB |  00m00s
[157/182] gdbm-libs-1:1.23-11.fc44.aarc 100% |   6.1 MiB/s |  56.3 KiB |  00m00s
[158/182] fedora-release-0:44-0.10.noar 100% |   1.9 MiB/s |  13.5 KiB |  00m00s
[159/182] cyrus-sasl-lib-0:2.1.28-35.fc 100% |   6.2 MiB/s | 772.9 KiB |  00m00s
[160/182] xxhash-libs-0:0.8.3-4.fc44.aa 100% | 244.3 KiB/s |  34.5 KiB |  00m00s
[161/182] fedora-release-identity-basic 100% |   2.0 MiB/s |  14.3 KiB |  00m00s
[162/182] systemd-standalone-sysusers-0 100% | 459.8 KiB/s | 138.4 KiB |  00m00s
[163/182] libcurl-0:8.18.0-3.fc44.aarch 100% |   3.0 MiB/s | 423.8 KiB |  00m00s
[164/182] libbrotli-0:1.2.0-3.fc44.aarc 100% |  37.8 MiB/s | 348.7 KiB |  00m00s
[165/182] libnghttp2-0:1.68.0-3.fc44.aa 100% |  10.4 MiB/s |  74.7 KiB |  00m00s
[166/182] libnghttp3-0:1.15.0-1.fc44.aa 100% |   9.6 MiB/s |  68.8 KiB |  00m00s
[167/182] libpsl-0:0.21.5-7.fc44.aarch6 100% |   7.9 MiB/s |  64.9 KiB |  00m00s
[168/182] gdb-minimal-0:17.1-2.fc44.aar 100% |  12.6 MiB/s |   4.4 MiB |  00m00s
[169/182] ngtcp2-0:1.19.0-2.fc44.aarch6 100% |  17.7 MiB/s | 144.9 KiB |  00m00s
[170/182] ngtcp2-crypto-ossl-0:1.19.0-2 100% |   2.8 MiB/s |  25.6 KiB |  00m00s
[171/182] libssh-0:0.11.3-1.fc44.aarch6 100% |   5.2 MiB/s | 230.6 KiB |  00m00s
[172/182] keyutils-libs-0:1.6.3-7.fc44. 100% |   3.1 MiB/s |  31.5 KiB |  00m00s
[173/182] libcom_err-0:1.47.3-4.fc44.aa 100% |   3.8 MiB/s |  27.0 KiB |  00m00s
[174/182] libverto-0:0.3.2-12.fc44.aarc 100% |   2.2 MiB/s |  20.5 KiB |  00m00s
[175/182] publicsuffix-list-dafsa-0:202 100% |   7.4 MiB/s |  60.3 KiB |  00m00s
[176/182] libssh-config-0:0.11.3-1.fc44 100% |   1.0 MiB/s |   9.1 KiB |  00m00s
[177/182] krb5-libs-0:1.21.3-12.fc44.aa 100% |   4.6 MiB/s | 752.1 KiB |  00m00s
[178/182] selinux-policy-0:42.22-1.fc44 100% |   9.5 MiB/s |  67.8 KiB |  00m00s
[179/182] libselinux-utils-0:3.9-7.fc44 100% |   1.1 MiB/s | 122.4 KiB |  00m00s
[180/182] policycoreutils-0:3.9-8.fc44. 100% |   1.2 MiB/s | 259.2 KiB |  00m00s
[181/182] rpm-plugin-selinux-0:6.0.1-2. 100% | 447.4 KiB/s |  19.2 KiB |  00m00s
[182/182] selinux-policy-targeted-0:42. 100% |  18.8 MiB/s |   6.8 MiB |  00m00s
--------------------------------------------------------------------------------
[182/182] Total                         100% |  13.9 MiB/s |  65.9 MiB |  00m05s
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% | 755.0   B/s | 182.0   B |  00m00s
[  2/184] Prepare transaction           100% |   2.3 KiB/s | 182.0   B |  00m00s
[  3/184] Installing libgcc-0:16.0.1-0. 100% | 109.3 MiB/s | 223.9 KiB |  00m00s
[  4/184] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/184] Installing publicsuffix-list- 100% |  69.4 MiB/s |  71.1 KiB |  00m00s
[  6/184] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0   B |  00m00s
[  7/184] Installing fedora-gpg-keys-0: 100% |  29.1 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% |  39.6 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/184] Installing filesystem-0:3.18- 100% |   2.0 MiB/s | 212.8 KiB |  00m00s
[ 14/184] Installing pkgconf-m4-0:2.3.0 100% |  14.5 MiB/s |  14.8 KiB |  00m00s
[ 15/184] Installing pcre2-syntax-0:10. 100% | 138.8 MiB/s | 284.3 KiB |  00m00s
[ 16/184] Installing gnulib-l10n-0:2024 100% | 129.3 MiB/s | 661.9 KiB |  00m00s
[ 17/184] Installing coreutils-common-0 100% | 303.5 MiB/s |  11.2 MiB |  00m00s
[ 18/184] Installing ncurses-base-0:6.5 100% |  49.3 MiB/s | 353.5 KiB |  00m00s
[ 19/184] Installing bash-0:5.3.9-3.fc4 100% | 210.8 MiB/s |   8.4 MiB |  00m00s
[ 20/184] Installing glibc-common-0:2.4 100% |  57.6 MiB/s |   1.3 MiB |  00m00s
[ 21/184] Installing glibc-gconv-extra- 100% | 388.1 MiB/s |  18.6 MiB |  00m00s
[ 22/184] Installing glibc-0:2.42.9000- 100% | 145.1 MiB/s |   6.4 MiB |  00m00s
[ 23/184] Installing ncurses-libs-0:6.5 100% | 249.2 MiB/s |   1.2 MiB |  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% | 131.0 MiB/s | 134.2 KiB |  00m00s
[ 26/184] Installing bzip2-libs-0:1.0.8 100% |  71.9 MiB/s |  73.6 KiB |  00m00s
[ 27/184] Installing libgpg-error-0:1.5 100% |  46.3 MiB/s | 995.5 KiB |  00m00s
[ 28/184] Installing libstdc++-0:16.0.1 100% | 315.9 MiB/s |   2.8 MiB |  00m00s
[ 29/184] Installing libassuan-0:2.5.7- 100% | 106.3 MiB/s | 217.7 KiB |  00m00s
[ 30/184] Installing libgcrypt-0:1.11.2 100% | 239.1 MiB/s |   1.2 MiB |  00m00s
[ 31/184] Installing readline-0:8.3-4.f 100% | 184.1 MiB/s | 565.6 KiB |  00m00s
[ 32/184] Installing gmp-1:6.3.0-5.fc44 100% | 214.9 MiB/s | 660.1 KiB |  00m00s
[ 33/184] Installing libuuid-0:2.41.3-1 100% |  68.6 MiB/s |  70.3 KiB |  00m00s
[ 34/184] Installing xz-libs-1:5.8.2-2. 100% | 130.1 MiB/s | 266.5 KiB |  00m00s
[ 35/184] Installing popt-0:1.19-10.fc4 100% |  36.9 MiB/s | 151.3 KiB |  00m00s
[ 36/184] Installing libzstd-0:1.5.7-5. 100% | 280.4 MiB/s | 861.5 KiB |  00m00s
[ 37/184] Installing elfutils-libelf-0: 100% | 286.1 MiB/s |   1.1 MiB |  00m00s
[ 38/184] Installing npth-0:1.8-4.fc44. 100% |  92.2 MiB/s |  94.4 KiB |  00m00s
[ 39/184] Installing libblkid-0:2.41.3- 100% | 142.3 MiB/s | 291.4 KiB |  00m00s
[ 40/184] Installing systemd-libs-0:259 100% | 307.6 MiB/s |   2.5 MiB |  00m00s
[ 41/184] Installing libxcrypt-0:4.5.2- 100% | 134.7 MiB/s | 275.9 KiB |  00m00s
[ 42/184] Installing libsepol-0:3.9-3.f 100% | 263.9 MiB/s | 810.6 KiB |  00m00s
[ 43/184] Installing sqlite-libs-0:3.51 100% | 261.2 MiB/s |   1.6 MiB |  00m00s
[ 44/184] Installing gnupg2-gpgconf-0:2 100% |  18.6 MiB/s | 323.8 KiB |  00m00s
[ 45/184] Installing libattr-0:2.5.2-8. 100% |  67.6 MiB/s |  69.3 KiB |  00m00s
[ 46/184] Installing libacl-0:2.3.2-6.f 100% |  67.0 MiB/s |  68.6 KiB |  00m00s
[ 47/184] Installing pcre2-0:10.47-1.fc 100% | 233.0 MiB/s | 715.7 KiB |  00m00s
[ 48/184] Installing libselinux-0:3.9-7 100% |  98.7 MiB/s | 202.2 KiB |  00m00s
[ 49/184] Installing grep-0:3.12-3.fc44 100% |  47.2 MiB/s |   1.0 MiB |  00m00s
[ 50/184] Installing sed-0:4.9-7.fc44.a 100% |  41.0 MiB/s | 881.3 KiB |  00m00s
[ 51/184] Installing findutils-1:4.10.0 100% |  80.0 MiB/s |   1.9 MiB |  00m00s
[ 52/184] Installing libtasn1-0:4.20.0- 100% | 108.4 MiB/s | 222.0 KiB |  00m00s
[ 53/184] Installing libunistring-0:1.1 100% | 291.0 MiB/s |   1.7 MiB |  00m00s
[ 54/184] Installing libidn2-0:2.3.8-3. 100% |  55.3 MiB/s | 566.6 KiB |  00m00s
[ 55/184] Installing crypto-policies-0: 100% |  22.0 MiB/s | 157.7 KiB |  00m00s
[ 56/184] Installing xz-1:5.8.2-2.fc44. 100% |  57.9 MiB/s |   1.4 MiB |  00m00s
[ 57/184] Installing libmount-0:2.41.3- 100% | 205.7 MiB/s | 421.2 KiB |  00m00s
[ 58/184] Installing gnupg2-verify-0:2. 100% |  19.8 MiB/s | 365.7 KiB |  00m00s
[ 59/184] Installing dwz-0:0.16-3.fc44. 100% |  18.6 MiB/s | 323.8 KiB |  00m00s
[ 60/184] Installing mpfr-0:4.2.2-3.fc4 100% | 184.8 MiB/s | 757.1 KiB |  00m00s
[ 61/184] Installing gawk-0:5.3.2-3.fc4 100% |  99.2 MiB/s |   2.6 MiB |  00m00s
[ 62/184] Installing libksba-0:1.6.7-5. 100% | 130.5 MiB/s | 400.8 KiB |  00m00s
[ 63/184] Installing unzip-0:6.0-69.fc4 100% |  29.2 MiB/s | 537.3 KiB |  00m00s
[ 64/184] Installing file-libs-0:5.46-9 100% | 594.0 MiB/s |  11.9 MiB |  00m00s
[ 65/184] Installing file-0:5.46-9.fc44 100% |   8.1 MiB/s | 141.6 KiB |  00m00s
[ 66/184] Installing diffutils-0:3.12-5 100% |  70.6 MiB/s |   1.6 MiB |  00m00s
[ 67/184] Installing libeconf-0:0.7.9-3 100% |  80.5 MiB/s |  82.5 KiB |  00m00s
[ 68/184] Installing libcap-ng-0:0.9-5. 100% | 158.7 MiB/s | 162.5 KiB |  00m00s
[ 69/184] Installing audit-libs-0:4.1.2 100% | 238.8 MiB/s | 489.1 KiB |  00m00s
[ 70/184] Installing pam-libs-0:1.7.2-1 100% | 109.8 MiB/s | 225.0 KiB |  00m00s
[ 71/184] Installing libcap-0:2.77-2.fc 100% |  26.4 MiB/s | 513.1 KiB |  00m00s
[ 72/184] Installing libsemanage-0:3.9- 100% | 176.6 MiB/s | 361.7 KiB |  00m00s
[ 73/184] Installing libsmartcols-0:2.4 100% | 220.2 MiB/s | 225.5 KiB |  00m00s
[ 74/184] Installing alternatives-0:1.3 100% |   5.6 MiB/s |  91.6 KiB |  00m00s
[ 75/184] Installing lua-libs-0:5.4.8-5 100% | 161.7 MiB/s | 331.3 KiB |  00m00s
[ 76/184] Installing libffi-0:3.5.2-2.f 100% |  76.7 MiB/s | 157.1 KiB |  00m00s
[ 77/184] Installing p11-kit-0:0.25.8-2 100% |  93.0 MiB/s |   2.5 MiB |  00m00s
[ 78/184] Installing p11-kit-trust-0:0. 100% |  21.6 MiB/s | 531.7 KiB |  00m00s
[ 79/184] Installing json-c-0:0.18-8.fc 100% | 136.5 MiB/s | 139.7 KiB |  00m00s
[ 80/184] Installing ngtcp2-0:1.19.0-2. 100% | 167.3 MiB/s | 342.5 KiB |  00m00s
[ 81/184] Installing openssl-libs-1:3.5 100% | 309.2 MiB/s |   7.4 MiB |  00m00s
[ 82/184] Installing coreutils-0:9.9-4. 100% | 181.2 MiB/s |   8.2 MiB |  00m00s
[ 83/184] Installing ca-certificates-0: 100% |   1.5 MiB/s |   2.5 MiB |  00m02s
[ 84/184] Installing gzip-0:1.14-2.fc44 100% |  22.8 MiB/s | 443.0 KiB |  00m00s
[ 85/184] Installing rpm-sequoia-0:1.10 100% | 288.3 MiB/s |   2.3 MiB |  00m00s
[ 86/184] Installing libfsverity-0:1.6- 100% |  67.7 MiB/s |  69.3 KiB |  00m00s
[ 87/184] Installing libevent-0:2.1.12- 100% | 271.2 MiB/s |   1.1 MiB |  00m00s
[ 88/184] Installing ngtcp2-crypto-ossl 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 89/184] Installing util-linux-core-0: 100% |  96.0 MiB/s |   2.4 MiB |  00m00s
[ 90/184] Installing zip-0:3.0-45.fc44. 100% |  39.4 MiB/s | 765.8 KiB |  00m00s
[ 91/184] Installing gnupg2-keyboxd-0:2 100% |  38.2 MiB/s | 234.5 KiB |  00m00s
[ 92/184] Installing libpsl-0:0.21.5-7. 100% | 130.3 MiB/s | 133.4 KiB |  00m00s
[ 93/184] Installing tar-2:1.35-8.fc44. 100% | 107.3 MiB/s |   3.0 MiB |  00m00s
[ 94/184] Installing linkdupes-0:0.7.2- 100% |  40.1 MiB/s | 780.6 KiB |  00m00s
[ 95/184] Installing libselinux-utils-0 100% |  64.6 MiB/s |   1.4 MiB |  00m00s
[ 96/184] Installing liblastlog2-0:2.41 100% |  22.7 MiB/s | 139.6 KiB |  00m00s
[ 97/184] Installing systemd-standalone 100% |  17.9 MiB/s | 330.1 KiB |  00m00s
[ 98/184] Installing rpm-libs-0:6.0.1-2 100% | 243.3 MiB/s | 996.5 KiB |  00m00s
[ 99/184] Installing libusb1-0:1.0.29-5 100% |  22.0 MiB/s | 180.5 KiB |  00m00s
>>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.aarch64
>>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-9.fc44.aarch64
>>> 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% | 239.7 MiB/s |   2.2 MiB |  00m00s
[101/184] Installing ima-evm-utils-libs 100% |  91.7 MiB/s |  93.9 KiB |  00m00s
[102/184] Installing gnupg2-gpg-agent-0 100% |  31.9 MiB/s | 850.6 KiB |  00m00s
[103/184] Installing libfdisk-0:2.41.3- 100% | 102.5 MiB/s | 419.7 KiB |  00m00s
[104/184] Installing util-linux-0:2.41. 100% | 137.1 MiB/s |   6.9 MiB |  00m00s
[105/184] Installing policycoreutils-0: 100% |  43.7 MiB/s |   1.5 MiB |  00m00s
[106/184] Installing selinux-policy-0:4 100% |   1.4 MiB/s |  33.6 KiB |  00m00s
[107/184] Installing selinux-policy-tar 100% | 129.8 MiB/s |  14.8 MiB |  00m00s
[108/184] Installing zstd-0:1.5.7-5.fc4 100% |  26.3 MiB/s | 565.8 KiB |  00m00s
[109/184] Installing libxml2-0:2.12.10- 100% |  82.2 MiB/s |   1.9 MiB |  00m00s
[110/184] Installing nettle-0:3.10.1-3. 100% | 250.1 MiB/s | 768.2 KiB |  00m00s
[111/184] Installing gnutls-0:3.8.11-10 100% | 297.6 MiB/s |   3.6 MiB |  00m00s
[112/184] Installing bzip2-0:1.0.8-23.f 100% |  10.1 MiB/s | 175.6 KiB |  00m00s
[113/184] Installing add-determinism-0: 100% |  90.0 MiB/s |   2.0 MiB |  00m00s
[114/184] Installing build-reproducibil 100% |   1.5 MiB/s |   1.5 KiB |  00m00s
[115/184] Installing cpio-0:2.15-6.fc43 100% |  49.8 MiB/s |   1.1 MiB |  00m00s
[116/184] Installing ed-0:1.22.4-2.fc44 100% |   9.2 MiB/s | 159.4 KiB |  00m00s
[117/184] Installing patch-0:2.8-4.fc44 100% |  15.2 MiB/s | 263.9 KiB |  00m00s
[118/184] Installing jansson-0:2.14-4.f 100% |  92.2 MiB/s |  94.4 KiB |  00m00s
[119/184] Installing lz4-libs-0:1.10.0- 100% | 193.7 MiB/s | 198.4 KiB |  00m00s
[120/184] Installing libarchive-0:3.8.4 100% | 238.5 MiB/s | 977.0 KiB |  00m00s
[121/184] Installing libgomp-0:16.0.1-0 100% | 289.2 MiB/s | 592.3 KiB |  00m00s
[122/184] Installing libpkgconf-0:2.3.0 100% | 131.8 MiB/s | 135.0 KiB |  00m00s
[123/184] Installing pkgconf-0:2.3.0-4. 100% |   6.6 MiB/s | 114.8 KiB |  00m00s
[124/184] Installing pkgconf-pkg-config 100% | 110.8 KiB/s |   1.8 KiB |  00m00s
[125/184] Installing libtool-ltdl-0:2.5 100% |  92.8 MiB/s |  95.0 KiB |  00m00s
[126/184] Installing gdbm-libs-1:1.23-1 100% | 229.9 MiB/s | 235.4 KiB |  00m00s
[127/184] Installing cyrus-sasl-lib-0:2 100% | 100.7 MiB/s |   2.4 MiB |  00m00s
[128/184] Installing openldap-0:2.6.10- 100% | 186.9 MiB/s | 765.4 KiB |  00m00s
[129/184] Installing gnupg2-dirmngr-0:2 100% |  25.3 MiB/s | 648.8 KiB |  00m00s
[130/184] Installing gnupg2-0:2.4.9-4.f 100% | 174.5 MiB/s |   6.5 MiB |  00m00s
[131/184] Installing rpm-sign-libs-0:6. 100% |  66.8 MiB/s |  68.5 KiB |  00m00s
[132/184] Installing gpgverify-0:2.2-4. 100% |   9.2 MiB/s |   9.4 KiB |  00m00s
[133/184] Installing xxhash-libs-0:0.8. 100% |  85.1 MiB/s |  87.2 KiB |  00m00s
[134/184] Installing libbrotli-0:1.2.0- 100% | 222.5 MiB/s | 911.3 KiB |  00m00s
[135/184] Installing libnghttp2-0:1.68. 100% | 194.3 MiB/s | 199.0 KiB |  00m00s
[136/184] Installing libnghttp3-0:1.15. 100% | 203.1 MiB/s | 208.0 KiB |  00m00s
[137/184] Installing keyutils-libs-0:1. 100% |  97.3 MiB/s |  99.6 KiB |  00m00s
[138/184] Installing libcom_err-0:1.47. 100% | 109.5 MiB/s | 112.1 KiB |  00m00s
[139/184] Installing libverto-0:0.3.2-1 100% |  69.4 MiB/s |  71.1 KiB |  00m00s
[140/184] Installing krb5-libs-0:1.21.3 100% | 253.1 MiB/s |   2.5 MiB |  00m00s
[141/184] Installing libssh-0:0.11.3-1. 100% | 191.8 MiB/s | 589.1 KiB |  00m00s
[142/184] Installing libcurl-0:8.18.0-3 100% | 239.7 MiB/s | 982.0 KiB |  00m00s
[143/184] Installing curl-0:8.18.0-3.fc 100% |  16.9 MiB/s | 466.7 KiB |  00m00s
[144/184] Installing rpm-0:6.0.1-2.fc44 100% |  63.5 MiB/s |   2.8 MiB |  00m00s
[145/184] Installing cmake-srpm-macros- 100% | 785.2 KiB/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% |   9.1 MiB/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% |  38.0 MiB/s |  38.9 KiB |  00m00s
[152/184] Installing elfutils-default-y 100% | 408.6 KiB/s |   2.0 KiB |  00m00s
[153/184] Installing elfutils-libs-0:0. 100% | 182.7 MiB/s | 748.2 KiB |  00m00s
[154/184] Installing elfutils-debuginfo 100% |   7.5 MiB/s | 146.0 KiB |  00m00s
[155/184] Installing binutils-0:2.45.50 100% | 284.3 MiB/s |  30.7 MiB |  00m00s
[156/184] Installing elfutils-0:0.194-3 100% | 125.5 MiB/s |   3.3 MiB |  00m00s
[157/184] Installing gdb-minimal-0:17.1 100% | 231.6 MiB/s |  13.7 MiB |  00m00s
[158/184] Installing debugedit-0:5.2-6. 100% |  17.4 MiB/s | 321.6 KiB |  00m00s
[159/184] Installing rpm-build-libs-0:6 100% | 129.3 MiB/s | 264.8 KiB |  00m00s
[160/184] Installing rust-srpm-macros-0 100% |   6.2 MiB/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% |  35.4 MiB/s |  36.2 KiB |  00m00s
[173/184] Installing redhat-rpm-config- 100% |  61.8 MiB/s | 189.9 KiB |  00m00s
[174/184] Installing forge-srpm-macros- 100% |  39.3 MiB/s |  40.3 KiB |  00m00s
[175/184] Installing fonts-srpm-macros- 100% |  55.7 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% |  29.7 MiB/s | 607.4 KiB |  00m00s
[178/184] Installing pyproject-srpm-mac 100% |   2.4 MiB/s |   2.5 KiB |  00m00s
[179/184] Installing R-srpm-macros-0:1. 100% | 699.9 KiB/s |   4.2 KiB |  00m00s
[180/184] Installing python-srpm-macros 100% |  51.7 MiB/s |  52.9 KiB |  00m00s
[181/184] Installing rpm-plugin-selinux 100% |  67.3 MiB/s |  68.9 KiB |  00m00s
[182/184] Installing which-0:2.23-4.fc4 100% |   6.5 MiB/s | 125.5 KiB |  00m00s
[183/184] Installing shadow-utils-2:4.1 100% | 104.5 MiB/s |   4.5 MiB |  00m00s
[184/184] Installing info-0:7.2-7.fc44. 100% |  48.8 KiB/s | 422.0 KiB |  00m09s
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.aarch64
alternatives-1.33-5.fc44.aarch64
ansible-srpm-macros-1-20.1.fc44.noarch
audit-libs-4.1.2-4.fc44.aarch64
bash-5.3.9-3.fc44.aarch64
binutils-2.45.50-19.fc44.aarch64
build-reproducibility-srpm-macros-0.7.2-3.fc44.noarch
bzip2-1.0.8-23.fc44.aarch64
bzip2-libs-1.0.8-23.fc44.aarch64
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.aarch64
coreutils-common-9.9-4.fc44.aarch64
cpio-2.15-6.fc43.aarch64
crypto-policies-20251128-3.git19878fe.fc44.noarch
curl-8.18.0-3.fc44.aarch64
cyrus-sasl-lib-2.1.28-35.fc44.aarch64
debugedit-5.2-6.fc44.aarch64
diffutils-3.12-5.fc44.aarch64
dwz-0.16-3.fc44.aarch64
ed-1.22.4-2.fc44.aarch64
efi-srpm-macros-6-6.fc44.noarch
elfutils-0.194-3.fc44.aarch64
elfutils-debuginfod-client-0.194-3.fc44.aarch64
elfutils-default-yama-scope-0.194-3.fc44.noarch
elfutils-libelf-0.194-3.fc44.aarch64
elfutils-libs-0.194-3.fc44.aarch64
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.aarch64
file-libs-5.46-9.fc44.aarch64
filesystem-3.18-52.fc44.aarch64
filesystem-srpm-macros-3.18-52.fc44.noarch
findutils-4.10.0-7.fc44.aarch64
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.aarch64
gdb-minimal-17.1-2.fc44.aarch64
gdbm-libs-1.23-11.fc44.aarch64
ghc-srpm-macros-1.9.2-4.fc44.noarch
glibc-2.42.9000-25.fc44.aarch64
glibc-common-2.42.9000-25.fc44.aarch64
glibc-gconv-extra-2.42.9000-25.fc44.aarch64
glibc-minimal-langpack-2.42.9000-25.fc44.aarch64
gmp-6.3.0-5.fc44.aarch64
gnat-srpm-macros-7-2.fc44.noarch
gnulib-l10n-20241231-2.fc44.noarch
gnupg2-2.4.9-4.fc44.aarch64
gnupg2-dirmngr-2.4.9-4.fc44.aarch64
gnupg2-gpg-agent-2.4.9-4.fc44.aarch64
gnupg2-gpgconf-2.4.9-4.fc44.aarch64
gnupg2-keyboxd-2.4.9-4.fc44.aarch64
gnupg2-verify-2.4.9-4.fc44.aarch64
gnutls-3.8.11-10.fc44.aarch64
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.aarch64
gzip-1.14-2.fc44.aarch64
ima-evm-utils-libs-1.6.2-8.fc44.aarch64
info-7.2-7.fc44.aarch64
jansson-2.14-4.fc44.aarch64
java-srpm-macros-1-8.fc44.noarch
json-c-0.18-8.fc44.aarch64
kernel-srpm-macros-1.0-28.fc44.noarch
keyutils-libs-1.6.3-7.fc44.aarch64
krb5-libs-1.21.3-12.fc44.aarch64
libacl-2.3.2-6.fc44.aarch64
libarchive-3.8.4-2.fc44.aarch64
libassuan-2.5.7-5.fc44.aarch64
libattr-2.5.2-8.fc44.aarch64
libblkid-2.41.3-12.fc44.aarch64
libbrotli-1.2.0-3.fc44.aarch64
libcap-2.77-2.fc44.aarch64
libcap-ng-0.9-5.fc44.aarch64
libcom_err-1.47.3-4.fc44.aarch64
libcurl-8.18.0-3.fc44.aarch64
libeconf-0.7.9-3.fc44.aarch64
libevent-2.1.12-17.fc44.aarch64
libfdisk-2.41.3-12.fc44.aarch64
libffi-3.5.2-2.fc44.aarch64
libfsverity-1.6-4.fc44.aarch64
libgcc-16.0.1-0.3.fc44.1.aarch64
libgcrypt-1.11.2-1.fc44.aarch64
libgomp-16.0.1-0.3.fc44.1.aarch64
libgpg-error-1.58-2.fc44.aarch64
libidn2-2.3.8-3.fc44.aarch64
libksba-1.6.7-5.fc44.aarch64
liblastlog2-2.41.3-12.fc44.aarch64
libmount-2.41.3-12.fc44.aarch64
libnghttp2-1.68.0-3.fc44.aarch64
libnghttp3-1.15.0-1.fc44.aarch64
libpkgconf-2.3.0-4.fc44.aarch64
libpsl-0.21.5-7.fc44.aarch64
libselinux-3.9-7.fc44.aarch64
libselinux-utils-3.9-7.fc44.aarch64
libsemanage-3.9-5.fc44.aarch64
libsepol-3.9-3.fc44.aarch64
libsmartcols-2.41.3-12.fc44.aarch64
libssh-0.11.3-1.fc44.aarch64
libssh-config-0.11.3-1.fc44.noarch
libstdc++-16.0.1-0.3.fc44.1.aarch64
libtasn1-4.20.0-3.fc44.aarch64
libtool-ltdl-2.5.4-10.fc44.aarch64
libunistring-1.1-11.fc44.aarch64
libusb1-1.0.29-5.fc44.aarch64
libuuid-2.41.3-12.fc44.aarch64
libverto-0.3.2-12.fc44.aarch64
libxcrypt-4.5.2-3.fc44.aarch64
libxml2-2.12.10-6.fc44.aarch64
libzstd-1.5.7-5.fc44.aarch64
linkdupes-0.7.2-3.fc44.aarch64
lua-libs-5.4.8-5.fc44.aarch64
lua-srpm-macros-1-17.fc44.noarch
lz4-libs-1.10.0-4.fc44.aarch64
mpfr-4.2.2-3.fc44.aarch64
ncurses-base-6.5-9.20250614.fc44.noarch
ncurses-libs-6.5-9.20250614.fc44.aarch64
nettle-3.10.1-3.fc44.aarch64
ngtcp2-1.19.0-2.fc44.aarch64
ngtcp2-crypto-ossl-1.19.0-2.fc44.aarch64
npth-1.8-4.fc44.aarch64
ocaml-srpm-macros-11-3.fc44.noarch
openblas-srpm-macros-2-21.fc44.noarch
openldap-2.6.10-7.fc44.aarch64
openssl-libs-3.5.4-2.fc44.aarch64
p11-kit-0.25.8-2.fc44.aarch64
p11-kit-trust-0.25.8-2.fc44.aarch64
package-notes-srpm-macros-0.5-15.fc44.noarch
pam-libs-1.7.2-1.fc44.aarch64
patch-2.8-4.fc44.aarch64
pcre2-10.47-1.fc44.1.aarch64
pcre2-syntax-10.47-1.fc44.1.noarch
perl-srpm-macros-1-61.fc44.noarch
pkgconf-2.3.0-4.fc44.aarch64
pkgconf-m4-2.3.0-4.fc44.noarch
pkgconf-pkg-config-2.3.0-4.fc44.aarch64
policycoreutils-3.9-8.fc44.aarch64
popt-1.19-10.fc44.aarch64
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.aarch64
redhat-rpm-config-343-19.fc44.noarch
rpm-6.0.1-2.fc44.aarch64
rpm-build-6.0.1-2.fc44.aarch64
rpm-build-libs-6.0.1-2.fc44.aarch64
rpm-libs-6.0.1-2.fc44.aarch64
rpm-plugin-selinux-6.0.1-2.fc44.aarch64
rpm-sequoia-1.10.0-2.fc44.aarch64
rpm-sign-libs-6.0.1-2.fc44.aarch64
rust-srpm-macros-28.4-3.fc44.noarch
sed-4.9-7.fc44.aarch64
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.aarch64
sqlite-libs-3.51.2-1.fc44.aarch64
systemd-libs-259-9.fc44.aarch64
systemd-standalone-sysusers-259-9.fc44.aarch64
tar-1.35-8.fc44.aarch64
tpm2-tss-4.1.3-9.fc44.aarch64
tree-sitter-srpm-macros-0.4.2-2.fc44.noarch
unzip-6.0-69.fc44.aarch64
util-linux-2.41.3-12.fc44.aarch64
util-linux-core-2.41.3-12.fc44.aarch64
which-2.23-4.fc44.aarch64
xxhash-libs-0.8.3-4.fc44.aarch64
xz-5.8.2-2.fc44.aarch64
xz-libs-5.8.2-2.fc44.aarch64
zig-srpm-macros-1-8.fc44.noarch
zip-3.0-45.fc44.aarch64
zlib-ng-compat-2.3.2-3.fc44.aarch64
zstd-1.5.7-5.fc44.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
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-aarch64-1769507958.610212/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-3cpn7ejv/htslib/htslib.spec) Config(child) 0 minutes 32 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-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1769507958.610212/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1769507958.610212/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-aarch64-1769507958.610212/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.aarch64
  rpm-sequoia-1.10.0-2.fc44.aarch64
  dnf5-5.3.0.0-7.fc44.aarch64
  dnf5-plugins-5.3.0.0-7.fc44.aarch64
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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/htslib-1.23-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |   3.3 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% |  23.2 KiB/s |  12.2 KiB |  00m01s
Repositories loaded.
Package                   Arch    Version                Repository      Size
Installing:
 bzip2-devel              aarch64 0:1.0.8-23.fc44        fedora     309.8 KiB
 gcc                      aarch64 0:16.0.1-0.3.fc44.1    fedora     110.6 MiB
 libcurl-devel            aarch64 0:8.18.0-3.fc44        fedora       1.4 MiB
 make                     aarch64 1:4.4.1-12.fc44        fedora       1.8 MiB
 openssl-devel            aarch64 1:3.5.4-2.fc44         fedora       4.6 MiB
 perl-Data-Dumper         aarch64 0:2.191-522.fc44       fedora     135.5 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         aarch64 4:5.42.0-521.fc44      fedora     174.5 KiB
 perl-lib                 aarch64 0:0.65-521.fc44        fedora       8.5 KiB
 xz-devel                 aarch64 1:5.8.2-2.fc44         fedora     258.8 KiB
 zlib-ng-compat-devel     aarch64 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       aarch64 0:13.05-3.fc44         fedora     707.7 KiB
 brotli                   aarch64 0:1.2.0-3.fc44         fedora      69.5 KiB
 brotli-devel             aarch64 0:1.2.0-3.fc44         fedora      65.9 KiB
 cmake-filesystem         aarch64 0:3.31.10-5.fc44       fedora       0.0   B
 cpp                      aarch64 0:16.0.1-0.3.fc44.1    fedora      39.9 MiB
 gcc-plugin-annobin       aarch64 0:16.0.1-0.3.fc44.1    fedora      69.2 KiB
 glibc-devel              aarch64 0:2.42.9000-25.fc44    fedora       2.3 MiB
 groff-base               aarch64 0:1.23.0-12.fc44       fedora       4.2 MiB
 kernel-headers           aarch64 0:6.19.0-0.rc6.43.fc44 fedora       6.8 MiB
 keyutils-libs-devel      aarch64 0:1.6.3-7.fc44         fedora      48.2 KiB
 krb5-devel               aarch64 0:1.21.3-12.fc44       fedora     705.9 KiB
 libasan                  aarch64 0:16.0.1-0.3.fc44.1    fedora       1.5 MiB
 libatomic                aarch64 0:16.0.1-0.3.fc44.1    fedora      77.4 KiB
 libcom_err-devel         aarch64 0:1.47.3-4.fc44        fedora      16.7 KiB
 libidn2-devel            aarch64 0:2.3.8-3.fc44         fedora     149.1 KiB
 libkadm5                 aarch64 0:1.21.3-12.fc44       fedora     265.8 KiB
 libmpc                   aarch64 0:1.3.1-9.fc44         fedora     152.5 KiB
 libnghttp2-devel         aarch64 0:1.68.0-3.fc44        fedora     288.0 KiB
 libnghttp3-devel         aarch64 0:1.15.0-1.fc44        fedora     107.4 KiB
 libpsl-devel             aarch64 0:0.21.5-7.fc44        fedora     110.2 KiB
 libselinux-devel         aarch64 0:3.9-7.fc44           fedora     121.6 KiB
 libsepol-devel           aarch64 0:3.9-3.fc44           fedora     121.4 KiB
 libssh-devel             aarch64 0:0.11.3-1.fc44        fedora     178.0 KiB
 libubsan                 aarch64 0:16.0.1-0.3.fc44.1    fedora     475.8 KiB
 libverto-devel           aarch64 0:0.3.2-12.fc44        fedora      25.7 KiB
 libxcrypt-devel          aarch64 0:4.5.2-3.fc44         fedora      31.0 KiB
 ncurses                  aarch64 0:6.5-9.20250614.fc44  fedora     892.7 KiB
 ngtcp2-crypto-ossl-devel aarch64 0:1.19.0-2.fc44        fedora       7.5 KiB
 ngtcp2-devel             aarch64 0:1.19.0-2.fc44        fedora     282.4 KiB
 pcre2-devel              aarch64 0:10.47-1.fc44.1       fedora       2.1 MiB
 pcre2-utf16              aarch64 0:10.47-1.fc44.1       fedora     582.9 KiB
 pcre2-utf32              aarch64 0:10.47-1.fc44.1       fedora     582.9 KiB
 perl-AutoLoader          noarch  0:5.74-521.fc44        fedora      20.6 KiB
 perl-B                   aarch64 0:1.89-521.fc44        fedora     545.2 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          aarch64 0:2.59-521.fc44        fedora     103.6 KiB
 perl-DynaLoader          aarch64 0:1.57-521.fc44        fedora      32.1 KiB
 perl-Encode              aarch64 4:3.21-521.fc44        fedora       4.8 MiB
 perl-Errno               aarch64 0:1.38-521.fc44        fedora       8.4 KiB
 perl-Exporter            noarch  0:5.79-521.fc44        fedora      54.3 KiB
 perl-Fcntl               aarch64 0:1.20-521.fc44        fedora      92.7 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                  aarch64 0:1.55-521.fc44        fedora     191.3 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         aarch64 0:3.16-521.fc44        fedora      93.9 KiB
 perl-Net-SSLeay          aarch64 0:1.94-12.fc44         fedora       1.4 MiB
 perl-POSIX               aarch64 0:2.23-521.fc44        fedora     263.3 KiB
 perl-PathTools           aarch64 0:3.94-521.fc44        fedora     223.9 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   aarch64 5:1.70-2.fc44          fedora     152.8 KiB
 perl-SelectSaver         noarch  0:1.02-521.fc44        fedora       2.2 KiB
 perl-Socket              aarch64 4:2.040-3.fc44         fedora     144.1 KiB
 perl-Storable            aarch64 1:3.37-522.fc44        fedora     243.1 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          aarch64 4:1.9778-521.fc44      fedora     151.6 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                aarch64 4:5.42.0-521.fc44      fedora      11.6 MiB
 perl-locale              noarch  0:1.13-521.fc44        fedora       6.1 KiB
 perl-mro                 aarch64 0:1.29-521.fc44        fedora      81.4 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:       101 packages

Total size of inbound packages is 72 MiB. Need to download 72 MiB.
After this operation, 206 MiB extra will be used (install 206 MiB, remove 0 B).
[  1/101] bzip2-devel-0:1.0.8-23.fc44.a 100% |   1.5 MiB/s | 213.6 KiB |  00m00s
[  2/101] libcurl-devel-0:8.18.0-3.fc44 100% |   2.9 MiB/s | 937.9 KiB |  00m00s
[  3/101] make-1:4.4.1-12.fc44.aarch64  100% |   2.7 MiB/s | 583.6 KiB |  00m00s
[  4/101] perl-Data-Dumper-0:2.191-522. 100% |   1.5 MiB/s |  55.2 KiB |  00m00s
[  5/101] perl-FindBin-0:1.54-521.fc44. 100% | 396.9 KiB/s |  13.9 KiB |  00m00s
[  6/101] perl-Getopt-Long-1:2.58-521.f 100% |   3.7 MiB/s |  63.6 KiB |  00m00s
[  7/101] perl-lib-0:0.65-521.fc44.aarc 100% | 297.0 KiB/s |  14.6 KiB |  00m00s
[  8/101] openssl-devel-1:3.5.4-2.fc44. 100% |  16.3 MiB/s |   3.0 MiB |  00m00s
[  9/101] xz-devel-1:5.8.2-2.fc44.aarch 100% |   1.1 MiB/s |  66.9 KiB |  00m00s
[ 10/101] zlib-ng-compat-devel-0:2.3.2- 100% | 826.0 KiB/s |  38.0 KiB |  00m00s
[ 11/101] perl-interpreter-4:5.42.0-521 100% | 400.0 KiB/s |  72.0 KiB |  00m00s
[ 12/101] glibc-devel-0:2.42.9000-25.fc 100% |   2.9 MiB/s | 604.7 KiB |  00m00s
[ 13/101] libasan-0:16.0.1-0.3.fc44.1.a 100% |   2.6 MiB/s | 494.6 KiB |  00m00s
[ 14/101] libatomic-0:16.0.1-0.3.fc44.1 100% | 238.1 KiB/s |  33.8 KiB |  00m00s
[ 15/101] libmpc-0:1.3.1-9.fc44.aarch64 100% |   1.1 MiB/s |  70.6 KiB |  00m00s
[ 16/101] libubsan-0:16.0.1-0.3.fc44.1. 100% |   4.3 MiB/s | 206.2 KiB |  00m00s
[ 17/101] brotli-devel-0:1.2.0-3.fc44.a 100% | 768.4 KiB/s |  34.6 KiB |  00m00s
[ 18/101] krb5-devel-0:1.21.3-12.fc44.a 100% |   3.6 MiB/s | 142.2 KiB |  00m00s
[ 19/101] libidn2-devel-0:2.3.8-3.fc44. 100% | 928.8 KiB/s |  64.1 KiB |  00m00s
[ 20/101] libnghttp2-devel-0:1.68.0-3.f 100% | 474.6 KiB/s |  54.6 KiB |  00m00s
[ 21/101] libnghttp3-devel-0:1.15.0-1.f 100% | 658.6 KiB/s |  26.3 KiB |  00m00s
[ 22/101] libpsl-devel-0:0.21.5-7.fc44. 100% |   1.1 MiB/s |  32.8 KiB |  00m00s
[ 23/101] libssh-devel-0:0.11.3-1.fc44. 100% | 197.0 KiB/s |  41.8 KiB |  00m00s
[ 24/101] ngtcp2-crypto-ossl-devel-0:1. 100% | 250.0 KiB/s |  11.0 KiB |  00m00s
[ 25/101] ngtcp2-devel-0:1.19.0-2.fc44. 100% |   1.4 MiB/s |  52.9 KiB |  00m00s
[ 26/101] perl-B-0:1.89-521.fc44.aarch6 100% |   2.3 MiB/s | 177.4 KiB |  00m00s
[ 27/101] perl-Carp-0:1.54-521.fc44.noa 100% |   1.7 MiB/s |  28.8 KiB |  00m00s
[ 28/101] perl-Exporter-0:5.79-521.fc44 100% |   1.8 MiB/s |  30.8 KiB |  00m00s
[ 29/101] perl-Scalar-List-Utils-5:1.70 100% | 562.5 KiB/s |  73.1 KiB |  00m00s
[ 30/101] perl-constant-0:1.33-522.fc44 100% | 880.8 KiB/s |  22.9 KiB |  00m00s
[ 31/101] cpp-0:16.0.1-0.3.fc44.1.aarch 100% |   5.5 MiB/s |  13.2 MiB |  00m02s
[ 32/101] perl-File-Basename-0:2.86-521 100% | 990.2 KiB/s |  16.8 KiB |  00m00s
[ 33/101] perl-libs-4:5.42.0-521.fc44.a 100% |   3.1 MiB/s |   2.5 MiB |  00m01s
[ 34/101] perl-Pod-Usage-4:2.05-521.fc4 100% |   2.3 MiB/s |  40.7 KiB |  00m00s
[ 35/101] perl-Text-ParseWords-0:3.31-5 100% | 294.2 KiB/s |  16.5 KiB |  00m00s
[ 36/101] perl-base-0:2.27-521.fc44.noa 100% | 882.1 KiB/s |  15.9 KiB |  00m00s
[ 37/101] perl-PathTools-0:3.94-521.fc4 100% | 772.0 KiB/s |  87.2 KiB |  00m00s
[ 38/101] perl-overload-0:1.40-521.fc44 100% |   2.5 MiB/s |  45.2 KiB |  00m00s
[ 39/101] cmake-filesystem-0:3.31.10-5. 100% | 282.0 KiB/s |  14.1 KiB |  00m00s
[ 40/101] libxcrypt-devel-0:4.5.2-3.fc4 100% |   1.3 MiB/s |  30.0 KiB |  00m00s
[ 41/101] brotli-0:1.2.0-3.fc44.aarch64 100% | 215.6 KiB/s |  23.7 KiB |  00m00s
[ 42/101] keyutils-libs-devel-0:1.6.3-7 100% |   1.6 MiB/s |  59.7 KiB |  00m00s
[ 43/101] gcc-0:16.0.1-0.3.fc44.1.aarch 100% |  11.7 MiB/s |  39.7 MiB |  00m03s
[ 44/101] libkadm5-0:1.21.3-12.fc44.aar 100% |   2.6 MiB/s |  77.2 KiB |  00m00s
[ 45/101] libcom_err-devel-0:1.47.3-4.f 100% | 199.9 KiB/s |  16.8 KiB |  00m00s
[ 46/101] libselinux-devel-0:3.9-7.fc44 100% |   2.2 MiB/s | 151.7 KiB |  00m00s
[ 47/101] publicsuffix-list-0:20260116- 100% |   1.8 MiB/s |  91.7 KiB |  00m00s
[ 48/101] perl-if-0:0.61.000-521.fc44.n 100% | 803.7 KiB/s |  13.7 KiB |  00m00s
[ 49/101] perl-overloading-0:0.02-521.f 100% | 739.0 KiB/s |  12.6 KiB |  00m00s
[ 50/101] libverto-devel-0:0.3.2-12.fc4 100% |  83.5 KiB/s |  14.4 KiB |  00m00s
[ 51/101] perl-DynaLoader-0:1.57-521.fc 100% | 656.9 KiB/s |  25.6 KiB |  00m00s
[ 52/101] perl-Errno-0:1.38-521.fc44.aa 100% | 427.9 KiB/s |  14.5 KiB |  00m00s
[ 53/101] kernel-headers-0:6.19.0-0.rc6 100% |   3.3 MiB/s |   1.7 MiB |  00m01s
[ 54/101] perl-Pod-Perldoc-0:3.28.01-52 100% |   4.9 MiB/s |  86.1 KiB |  00m00s
[ 55/101] perl-podlators-1:6.0.2-521.fc 100% |   7.0 MiB/s | 128.5 KiB |  00m00s
[ 56/101] perl-mro-0:1.29-521.fc44.aarc 100% | 612.7 KiB/s |  29.4 KiB |  00m00s
[ 57/101] libsepol-devel-0:3.9-3.fc44.a 100% | 764.9 KiB/s |  48.2 KiB |  00m00s
[ 58/101] perl-vars-0:1.05-521.fc44.noa 100% | 743.6 KiB/s |  12.6 KiB |  00m00s
[ 59/101] perl-Getopt-Std-0:1.14-521.fc 100% | 902.9 KiB/s |  15.3 KiB |  00m00s
[ 60/101] perl-MIME-Base64-0:3.16-521.f 100% | 964.8 KiB/s |  29.9 KiB |  00m00s
[ 61/101] perl-Storable-1:3.37-522.fc44 100% |   2.5 MiB/s |  95.7 KiB |  00m00s
[ 62/101] perl-parent-1:0.244-521.fc44. 100% | 826.7 KiB/s |  14.9 KiB |  00m00s
[ 63/101] pcre2-devel-0:10.47-1.fc44.1. 100% |   2.1 MiB/s | 550.9 KiB |  00m00s
[ 64/101] perl-Encode-4:3.21-521.fc44.a 100% |   2.4 MiB/s |   1.0 MiB |  00m00s
[ 65/101] perl-Fcntl-0:1.20-521.fc44.aa 100% | 396.8 KiB/s |  29.4 KiB |  00m00s
[ 66/101] perl-File-Temp-1:0.231.200-2. 100% |   2.9 MiB/s |  59.6 KiB |  00m00s
[ 67/101] perl-HTTP-Tiny-0:0.092-2.fc44 100% |   3.1 MiB/s |  57.2 KiB |  00m00s
[ 68/101] perl-IPC-Open3-0:1.24-521.fc4 100% |   1.2 MiB/s |  23.6 KiB |  00m00s
[ 69/101] perl-Pod-Simple-1:3.47-4.fc44 100% |  10.7 MiB/s | 220.0 KiB |  00m00s
[ 70/101] perl-IO-0:1.55-521.fc44.aarch 100% |   1.2 MiB/s |  81.8 KiB |  00m00s
[ 71/101] perl-Symbol-0:1.09-521.fc44.n 100% | 769.9 KiB/s |  13.9 KiB |  00m00s
[ 72/101] perl-Term-ANSIColor-0:5.01-52 100% |   2.2 MiB/s |  47.7 KiB |  00m00s
[ 73/101] perl-Term-Cap-0:1.18-521.fc44 100% |   1.3 MiB/s |  22.0 KiB |  00m00s
[ 74/101] perl-POSIX-0:2.23-521.fc44.aa 100% |   1.9 MiB/s |  97.1 KiB |  00m00s
[ 75/101] pcre2-utf16-0:10.47-1.fc44.1. 100% |   2.5 MiB/s | 230.2 KiB |  00m00s
[ 76/101] perl-File-Path-0:2.18-522.fc4 100% |   2.0 MiB/s |  35.3 KiB |  00m00s
[ 77/101] perl-IO-Socket-SSL-0:2.098-2. 100% |  12.1 MiB/s | 234.7 KiB |  00m00s
[ 78/101] perl-Net-SSLeay-0:1.94-12.fc4 100% |   3.7 MiB/s | 374.5 KiB |  00m00s
[ 79/101] pcre2-utf32-0:10.47-1.fc44.1. 100% | 958.4 KiB/s | 219.5 KiB |  00m00s
[ 80/101] perl-Socket-4:2.040-3.fc44.aa 100% |   1.6 MiB/s |  54.9 KiB |  00m00s
[ 81/101] perl-Time-Local-2:1.350-521.f 100% |   2.0 MiB/s |  34.5 KiB |  00m00s
[ 82/101] perl-File-stat-0:1.14-521.fc4 100% | 983.8 KiB/s |  16.7 KiB |  00m00s
[ 83/101] perl-SelectSaver-0:1.02-521.f 100% | 669.7 KiB/s |  11.4 KiB |  00m00s
[ 84/101] perl-Pod-Escapes-1:1.07-521.f 100% |   1.1 MiB/s |  19.8 KiB |  00m00s
[ 85/101] perl-Text-Tabs+Wrap-0:2024.00 100% |   1.1 MiB/s |  21.8 KiB |  00m00s
[ 86/101] perl-locale-0:1.13-521.fc44.n 100% | 774.2 KiB/s |  13.2 KiB |  00m00s
[ 87/101] groff-base-0:1.23.0-12.fc44.a 100% |   1.5 MiB/s |   1.1 MiB |  00m01s
[ 88/101] perl-Time-HiRes-4:1.9778-521. 100% | 361.0 KiB/s |  57.4 KiB |  00m00s
[ 89/101] perl-IO-Socket-IP-0:0.43-522. 100% |   2.2 MiB/s |  42.2 KiB |  00m00s
[ 90/101] perl-AutoLoader-0:5.74-521.fc 100% |   1.2 MiB/s |  20.9 KiB |  00m00s
[ 91/101] perl-Class-Struct-0:0.68-521. 100% |   1.2 MiB/s |  21.7 KiB |  00m00s
[ 92/101] perl-MIME-Base32-0:1.303-25.f 100% | 932.7 KiB/s |  20.5 KiB |  00m00s
[ 93/101] perl-libnet-0:3.15-522.fc44.n 100% |   6.6 MiB/s | 128.4 KiB |  00m00s
[ 94/101] perl-Digest-MD5-0:2.59-521.fc 100% | 775.1 KiB/s |  35.7 KiB |  00m00s
[ 95/101] perl-FileHandle-0:2.05-521.fc 100% | 797.7 KiB/s |  15.2 KiB |  00m00s
[ 96/101] perl-Digest-0:1.20-521.fc44.n 100% |   1.3 MiB/s |  24.9 KiB |  00m00s
[ 97/101] perl-URI-0:5.34-3.fc44.noarch 100% | 609.1 KiB/s | 149.2 KiB |  00m00s
[ 98/101] gcc-plugin-annobin-0:16.0.1-0 100% | 685.9 KiB/s |  37.0 KiB |  00m00s
[ 99/101] ncurses-0:6.5-9.20250614.fc44 100% |   1.2 MiB/s | 424.0 KiB |  00m00s
[100/101] annobin-docs-0:13.05-3.fc44.n 100% |   4.8 MiB/s |  88.9 KiB |  00m00s
[101/101] annobin-plugin-gcc-0:13.05-3. 100% |   2.6 MiB/s | 682.6 KiB |  00m00s
--------------------------------------------------------------------------------
[101/101] Total                         100% |  14.3 MiB/s |  71.6 MiB |  00m05s
Running transaction
[  1/103] Verify package files          100% | 431.0   B/s | 101.0   B |  00m00s
[  2/103] Prepare transaction           100% |   1.0 KiB/s | 101.0   B |  00m00s
[  3/103] Installing cmake-filesystem-0 100% |   3.7 MiB/s |   7.6 KiB |  00m00s
[  4/103] Installing ngtcp2-devel-0:1.1 100% | 277.0 MiB/s | 283.6 KiB |  00m00s
[  5/103] Installing libmpc-0:1.3.1-9.f 100% |  15.0 MiB/s | 154.0 KiB |  00m00s
[  6/103] Installing openssl-devel-1:3. 100% |  46.2 MiB/s |   5.6 MiB |  00m00s
[  7/103] Installing ngtcp2-crypto-ossl 100% |   7.9 MiB/s |   8.1 KiB |  00m00s
[  8/103] Installing cpp-0:16.0.1-0.3.f 100% | 260.8 MiB/s |  39.9 MiB |  00m00s
[  9/103] Installing zlib-ng-compat-dev 100% | 106.0 MiB/s | 108.6 KiB |  00m00s
[ 10/103] Installing libssh-devel-0:0.1 100% |  88.2 MiB/s | 180.6 KiB |  00m00s
[ 11/103] Installing annobin-docs-0:13. 100% |  98.0 MiB/s | 100.3 KiB |  00m00s
[ 12/103] Installing ncurses-0:6.5-9.20 100% |  41.8 MiB/s | 899.3 KiB |  00m00s
[ 13/103] Installing pcre2-utf32-0:10.4 100% | 190.0 MiB/s | 583.7 KiB |  00m00s
[ 14/103] Installing pcre2-utf16-0:10.4 100% | 190.0 MiB/s | 583.8 KiB |  00m00s
[ 15/103] Installing pcre2-devel-0:10.4 100% |  60.6 MiB/s |   2.1 MiB |  00m00s
[ 16/103] Installing groff-base-0:1.23. 100% |  99.9 MiB/s |   4.2 MiB |  00m00s
[ 17/103] Installing perl-Digest-0:1.20 100% |  36.2 MiB/s |  37.1 KiB |  00m00s
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Complete!
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Wrote: /builddir/build/SRPMS/htslib-1.23-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |   8.6 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% |  45.5 KiB/s |  12.2 KiB |  00m00s
Repositories loaded.
Package "bzip2-devel-1.0.8-23.fc44.aarch64" is already installed.
Package "gcc-16.0.1-0.3.fc44.1.aarch64" is already installed.
Package "libcurl-devel-8.18.0-3.fc44.aarch64" is already installed.
Package "make-1:4.4.1-12.fc44.aarch64" is already installed.
Package "openssl-devel-1:3.5.4-2.fc44.aarch64" is already installed.
Package "perl-Data-Dumper-2.191-522.fc44.aarch64" 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.aarch64" is already installed.Nothing to do.

Package "perl-interpreter-4:5.42.0-521.fc44.aarch64" is already installed.
Package "xz-devel-1:5.8.2-2.fc44.aarch64" is already installed.
Package "zlib-ng-compat-devel-2.3.2-3.fc44.aarch64" 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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1769040000
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.nHkTUf
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ZYSZRs
+ 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.W2g41l
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=aarch64-redhat-linux --host=aarch64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking for aarch64-redhat-linux-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for aarch64-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... no
checking whether __cpuid_count is declared... no
checking for x86intrin.h... no
checking for aarch64-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 aarch64-redhat-linux... plain .so
checking whether the linker supports versioned symbols... yes
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... aarch64-redhat-linux-gnu
checking host system type... aarch64-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... no
checking whether the compiler accepts -mbranch-protection=standard... yes
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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden  -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -mbranch-protection=standard -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/plugins-dlhts test/plugins-dlhts.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/test_time_funcs test/test_time_funcs.o
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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
      |                 ^
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 -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 -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_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm  -lcurl -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/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/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_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_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_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_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_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_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-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-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-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_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.tJQJmW
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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.aarch64 --unique-debug-src-base htslib-1.23-1.fc44.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --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.aarch64
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 208 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 208 files,
    considered 206 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.PkAwjd
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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/xlQFomYhIY/index.bam.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/xlQFomYhIY/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/xlQFomYhIY/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/xlQFomYhIY/index.bam.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/xlQFomYhIY/index.bam
.. ok

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

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

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/xlQFomYhIY/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/xlQFomYhIY/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/xlQFomYhIY/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/xlQFomYhIY/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/xlQFomYhIY/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/xlQFomYhIY/index.sam.gz
.. ok

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

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

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

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view  -p /tmp/xlQFomYhIY/index3_rgn.sam /tmp/xlQFomYhIY/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/xlQFomYhIY/index3_rgnm.sam /tmp/xlQFomYhIY/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/xlQFomYhIY/index.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/xlQFomYhIY/index.bcf
.. ok

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

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

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

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

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

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

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

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/xlQFomYhIY/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/xlQFomYhIY/index.bam.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/xlQFomYhIY/index.bam
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/xlQFomYhIY/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/xlQFomYhIY/index.bam.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/xlQFomYhIY/index.bam
.. ok

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

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

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/xlQFomYhIY/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/xlQFomYhIY/index.sam.gz.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/xlQFomYhIY/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -c /tmp/xlQFomYhIY/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/xlQFomYhIY/index.sam.gz.bai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index_dos.sam > /tmp/xlQFomYhIY/index.sam.gz
.. ok

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_index -b /tmp/xlQFomYhIY/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/xlQFomYhIY/index.cram.crai /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.sam > /tmp/xlQFomYhIY/index.cram
.. ok

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

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view -@4 -p /tmp/xlQFomYhIY/index3_rgn.sam /tmp/xlQFomYhIY/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/xlQFomYhIY/index3_rgnm.sam /tmp/xlQFomYhIY/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/xlQFomYhIY/index.bcf.csi /builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/index.vcf > /tmp/xlQFomYhIY/index.bcf
.. ok

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

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

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

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

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

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

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

test_index:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test_view /tmp/xlQFomYhIY/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/xlQFomYhIY/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/xlQFomYhIY/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/xlQFomYhIY -s 74452500
.. ok

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

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

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

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

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

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

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

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

test-bcf-sr:
	/builddir/build/BUILD/htslib-1.23-build/htslib-1.23/test/test-bcf-sr.pl -t /tmp/xlQFomYhIY -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/xlQFomYhIY/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/xlQFomYhIY/no_index_2.out 2> /tmp/xlQFomYhIY/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/xlQFomYhIY/no_index_3.out 2> /tmp/xlQFomYhIY/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/xlQFomYhIY/no_index_4.out 2> /tmp/xlQFomYhIY/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/xlQFomYhIY/weird-chr-names.vcf.bcf -x /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_1.out.vcf -r '1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_2.out.vcf -r '1:1-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_4.out.vcf -r '1:1-1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_5.out.vcf -r '{1:1}' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_14.out.vcf -t '1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_15.out.vcf -t '1:1-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_17.out.vcf -t '1:1-1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_18.out.vcf -t '{1:1}' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/xlQFomYhIY/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/xlQFomYhIY/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/xlQFomYhIY/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/xlQFomYhIY/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.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.8BpnTR
+ 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.LgoHyt
+ 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(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) 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_2.17)(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.aarch64
Provides: htslib-devel = 1.23-1.fc44 htslib-devel(aarch-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.aarch64
Provides: htslib-tools = 1.23-1.fc44 htslib-tools(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: htslib-debugsource-1.23-1.fc44.aarch64
Provides: htslib-debugsource = 1.23-1.fc44 htslib-debugsource(aarch-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.aarch64
Provides: debuginfo(build-id) = 361805625d561a16e4ea58b704244844bb7a76c1 debuginfo(build-id) = f2372c6beacf5f809244a05325404d08f13e6b19 debuginfo(build-id) = fc958a060035e02a6935abf7b47e30197acdbfc5 debuginfo(build-id) = fcbebfe87e69125ec5dd0eff3afcbe019f847cee htslib-debuginfo = 1.23-1.fc44 htslib-debuginfo(aarch-64) = 1.23-1.fc44 libhts.so.1.23-1.23-1.fc44.aarch64.debug()(64bit)
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: htslib-debugsource(aarch-64) = 1.23-1.fc44
Processing files: htslib-tools-debuginfo-1.23-1.fc44.aarch64
Provides: debuginfo(build-id) = 23b38f0805b4258e8f96899642702cc774bdfe5f debuginfo(build-id) = 29e3b7095542ea3bd38d8982636775a91b76a1eb debuginfo(build-id) = 496b9e159b4dd86cae61f79e9005a69db199af7f debuginfo(build-id) = aacc4461f839c48a2ee0667aee457faa06262325 debuginfo(build-id) = f7a9722ea16b0d02869596fa8ed4aa95be27d13d htslib-tools-debuginfo = 1.23-1.fc44 htslib-tools-debuginfo(aarch-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(aarch-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.aarch64.rpm
Wrote: /builddir/build/RPMS/htslib-tools-1.23-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/htslib-debugsource-1.23-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/htslib-devel-1.23-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/htslib-1.23-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.23-1.fc44.aarch64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Qz49fn
+ 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-aarch64-1769507958.610212/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 32 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-tools",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "htslib-debugsource",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "htslib",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "htslib-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "htslib-tools-debuginfo",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "htslib-devel",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "htslib",
            "epoch": null,
            "version": "1.23",
            "release": "1.fc44",
            "arch": "src"
        }
    ]
}
RPMResults finished