Warning: Permanently added '54.82.74.41' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-b5aj_zzz/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b5aj_zzz/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1746456050.955289 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.1 starting (python version = 3.13.0, NVR = mock-6.1-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-b5aj_zzz/bcftools/bcftools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b5aj_zzz/bcftools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1746456050.955289 -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-b5aj_zzz/bcftools/bcftools.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.1 INFO: Mock Version: 6.1 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1746456050.955289/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-a0aee162-98ef-4ba9-a2c7-211a761cdbf5 INFO: Checking that d1fd9f0d5d722dc475a6101e0a3a54850d8c5fa9ad07623795d2e07695725eb7 image matches host's architecture INFO: Copy content of container d1fd9f0d5d722dc475a6101e0a3a54850d8c5fa9ad07623795d2e07695725eb7 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1746456050.955289/root INFO: mounting d1fd9f0d5d722dc475a6101e0a3a54850d8c5fa9ad07623795d2e07695725eb7 with podman image mount INFO: image d1fd9f0d5d722dc475a6101e0a3a54850d8c5fa9ad07623795d2e07695725eb7 as /var/lib/containers/storage/overlay/a159a0e9c6b5ad626a7615265f538dfb24fbcb995f9e8a71d775bede951f0b6a/merged INFO: umounting image d1fd9f0d5d722dc475a6101e0a3a54850d8c5fa9ad07623795d2e07695725eb7 (/var/lib/containers/storage/overlay/a159a0e9c6b5ad626a7615265f538dfb24fbcb995f9e8a71d775bede951f0b6a/merged) with podman image umount INFO: Removing image mock-bootstrap-a0aee162-98ef-4ba9-a2c7-211a761cdbf5 INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1746456050.955289/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-5.99.90-4.fc43.x86_64 rpm-sequoia-1.8.0-1.fc43.x86_64 dnf5-5.2.13.1-1.fc43.x86_64 dnf5-plugins-5.2.13.1-1.fc43.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 139.7 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 56.6 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 1.8 MiB/s | 123.7 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-3.fc43 fedora 8.2 MiB bzip2 x86_64 1.0.8-20.fc42 fedora 99.3 KiB coreutils x86_64 9.7-1.fc43 fedora 5.4 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.12-1.fc43 fedora 1.6 MiB fedora-release-common noarch 43-0.15 fedora 20.4 KiB findutils x86_64 1:4.10.0-5.fc42 fedora 1.9 MiB gawk x86_64 5.3.2-1.fc43 fedora 1.8 MiB glibc-minimal-langpack x86_64 2.41.9000-12.fc43 fedora 0.0 B grep x86_64 3.12-1.fc43 fedora 1.0 MiB gzip x86_64 1.13-3.fc42 fedora 392.9 KiB info x86_64 7.2-3.fc42 fedora 357.9 KiB patch x86_64 2.8-1.fc43 fedora 226.8 KiB redhat-rpm-config noarch 343-4.fc43 fedora 185.6 KiB rpm-build x86_64 5.99.90-4.fc43 fedora 281.7 KiB sed x86_64 4.9-4.fc42 fedora 857.3 KiB shadow-utils x86_64 2:4.17.4-1.fc43 fedora 4.0 MiB tar x86_64 2:1.35-5.fc42 fedora 3.0 MiB unzip x86_64 6.0-66.fc42 fedora 390.3 KiB util-linux x86_64 2.40.4-7.fc43 fedora 3.4 MiB which x86_64 2.23-1.fc42 fedora 83.4 KiB xz x86_64 1:5.8.1-1.fc43 fedora 1.3 MiB Installing dependencies: add-determinism x86_64 0.6.0-1.fc43 fedora 2.5 MiB alternatives x86_64 1.32-1.fc43 fedora 62.2 KiB ansible-srpm-macros noarch 1-17.1.fc42 fedora 35.7 KiB audit-libs x86_64 4.0.3-2.fc42 fedora 351.3 KiB binutils x86_64 2.44-3.fc43 fedora 25.9 MiB build-reproducibility-srpm-macros noarch 0.6.0-1.fc43 fedora 735.0 B bzip2-libs x86_64 1.0.8-20.fc42 fedora 84.6 KiB ca-certificates noarch 2024.2.69_v8.0.401-5.fc42 fedora 2.6 MiB coreutils-common x86_64 9.7-1.fc43 fedora 11.3 MiB crypto-policies noarch 20250402-2.git86c0178.fc43 fedora 141.5 KiB curl x86_64 8.14.0~rc1-1.fc43 fedora 473.2 KiB cyrus-sasl-lib x86_64 2.1.28-30.fc42 fedora 2.3 MiB debugedit x86_64 5.1-6.fc43 fedora 192.7 KiB dwz x86_64 0.15-9.fc42 fedora 291.0 KiB ed x86_64 1.21-2.fc42 fedora 146.5 KiB efi-srpm-macros noarch 6-3.fc43 fedora 40.1 KiB elfutils x86_64 0.192-8.fc42 fedora 2.7 MiB elfutils-debuginfod-client x86_64 0.192-8.fc42 fedora 83.9 KiB elfutils-default-yama-scope noarch 0.192-8.fc42 fedora 1.8 KiB elfutils-libelf x86_64 0.192-8.fc42 fedora 1.2 MiB elfutils-libs x86_64 0.192-8.fc42 fedora 675.0 KiB fedora-gpg-keys noarch 43-0.2 fedora 129.0 KiB fedora-release noarch 43-0.15 fedora 0.0 B fedora-release-identity-basic noarch 43-0.15 fedora 664.0 B fedora-repos noarch 43-0.2 fedora 4.9 KiB fedora-repos-rawhide noarch 43-0.2 fedora 2.2 KiB file x86_64 5.46-1.fc42 fedora 100.2 KiB file-libs x86_64 5.46-1.fc42 fedora 11.9 MiB filesystem x86_64 3.18-40.fc43 fedora 112.0 B filesystem-srpm-macros noarch 3.18-40.fc43 fedora 38.2 KiB fonts-srpm-macros noarch 1:2.0.5-21.fc42 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-2.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-14.fc42 fedora 144.0 B gdb-minimal x86_64 16.3-1.fc43 fedora 13.2 MiB gdbm-libs x86_64 1:1.23-9.fc42 fedora 129.9 KiB ghc-srpm-macros noarch 1.9.2-2.fc42 fedora 779.0 B glibc x86_64 2.41.9000-12.fc43 fedora 6.7 MiB glibc-common x86_64 2.41.9000-12.fc43 fedora 1.0 MiB glibc-gconv-extra x86_64 2.41.9000-12.fc43 fedora 7.2 MiB gmp x86_64 1:6.3.0-3.fc43 fedora 819.2 KiB gnat-srpm-macros noarch 6-7.fc42 fedora 1.0 KiB gnupg2 x86_64 2.4.7-3.fc43 fedora 9.8 MiB gnutls x86_64 3.8.9-5.fc43 fedora 3.6 MiB go-srpm-macros noarch 3.6.0-7.fc43 fedora 60.8 KiB ima-evm-utils-libs x86_64 1.6.2-5.fc43 fedora 60.7 KiB jansson x86_64 2.14-2.fc42 fedora 93.1 KiB json-c x86_64 0.18-2.fc42 fedora 86.7 KiB kernel-srpm-macros noarch 1.0-25.fc42 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-5.fc42 fedora 58.3 KiB krb5-libs x86_64 1.21.3-5.fc42 fedora 2.3 MiB libacl x86_64 2.3.2-3.fc42 fedora 38.3 KiB libarchive x86_64 3.7.7-4.fc43 fedora 930.6 KiB libassuan x86_64 2.5.7-3.fc42 fedora 167.8 KiB libattr x86_64 2.5.2-5.fc42 fedora 27.1 KiB libblkid x86_64 2.40.4-7.fc43 fedora 262.4 KiB libbrotli x86_64 1.1.0-6.fc42 fedora 841.3 KiB libcap x86_64 2.76-1.fc43 fedora 209.2 KiB libcap-ng x86_64 0.8.5-4.fc42 fedora 72.9 KiB libcom_err x86_64 1.47.2-3.fc42 fedora 67.1 KiB libcurl x86_64 8.14.0~rc1-1.fc43 fedora 891.0 KiB libeconf x86_64 0.7.6-1.fc43 fedora 64.6 KiB libevent x86_64 2.1.12-15.fc42 fedora 903.1 KiB libfdisk x86_64 2.40.4-7.fc43 fedora 372.3 KiB libffi x86_64 3.4.7-4.fc43 fedora 82.6 KiB libfsverity x86_64 1.6-2.fc42 fedora 32.5 KiB libgcc x86_64 15.1.1-1.fc43 fedora 266.6 KiB libgcrypt x86_64 1.11.0-5.fc42 fedora 1.6 MiB libgomp x86_64 15.1.1-1.fc43 fedora 538.5 KiB libgpg-error x86_64 1.55-1.fc43 fedora 915.3 KiB libidn2 x86_64 2.3.8-1.fc43 fedora 552.5 KiB libksba x86_64 1.6.7-3.fc42 fedora 402.5 KiB libmount x86_64 2.40.4-7.fc43 fedora 356.2 KiB libnghttp2 x86_64 1.65.0-1.fc43 fedora 162.2 KiB libpkgconf x86_64 2.3.0-2.fc42 fedora 78.1 KiB libpsl x86_64 0.21.5-5.fc42 fedora 76.4 KiB libselinux x86_64 3.8-1.fc42 fedora 193.1 KiB libsemanage x86_64 3.8-1.fc42 fedora 308.4 KiB libsepol x86_64 3.8-1.fc42 fedora 826.0 KiB libsmartcols x86_64 2.40.4-7.fc43 fedora 180.4 KiB libssh x86_64 0.11.1-4.fc42 fedora 565.5 KiB libssh-config noarch 0.11.1-4.fc42 fedora 277.0 B libstdc++ x86_64 15.1.1-1.fc43 fedora 2.8 MiB libtasn1 x86_64 4.20.0-1.fc43 fedora 176.3 KiB libtool-ltdl x86_64 2.5.4-4.fc42 fedora 70.1 KiB libunistring x86_64 1.1-9.fc42 fedora 1.7 MiB libusb1 x86_64 1.0.28-2.fc43 fedora 171.0 KiB libuuid x86_64 2.40.4-7.fc43 fedora 37.3 KiB libverto x86_64 0.3.2-10.fc42 fedora 25.4 KiB libxcrypt x86_64 4.4.38-7.fc43 fedora 284.5 KiB libxml2 x86_64 2.12.10-1.fc43 fedora 1.7 MiB libzstd x86_64 1.5.7-1.fc43 fedora 807.8 KiB lua-libs x86_64 5.4.7-3.fc43 fedora 276.9 KiB lua-srpm-macros noarch 1-15.fc42 fedora 1.3 KiB lz4-libs x86_64 1.10.0-2.fc42 fedora 157.4 KiB mpfr x86_64 4.2.2-1.fc43 fedora 828.8 KiB ncurses-base noarch 6.5-5.20250125.fc42 fedora 326.8 KiB ncurses-libs x86_64 6.5-5.20250125.fc42 fedora 946.3 KiB nettle x86_64 3.10.1-1.fc43 fedora 790.5 KiB npth x86_64 1.8-2.fc42 fedora 49.6 KiB ocaml-srpm-macros noarch 10-4.fc42 fedora 1.9 KiB openblas-srpm-macros noarch 2-19.fc42 fedora 112.0 B openldap x86_64 2.6.9-5.fc43 fedora 655.1 KiB openssl-libs x86_64 1:3.5.0-3.fc43 fedora 8.9 MiB p11-kit x86_64 0.25.5-5.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-5.fc42 fedora 395.5 KiB package-notes-srpm-macros noarch 0.5-13.fc42 fedora 1.6 KiB pam-libs x86_64 1.7.0-4.fc42 fedora 126.7 KiB pcre2 x86_64 10.45-1.fc43 fedora 697.7 KiB pcre2-syntax noarch 10.45-1.fc43 fedora 273.9 KiB perl-srpm-macros noarch 1-58.fc43 copr_base 859.0 B pkgconf x86_64 2.3.0-2.fc42 fedora 88.5 KiB pkgconf-m4 noarch 2.3.0-2.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-2.fc42 fedora 989.0 B popt x86_64 1.19-8.fc42 fedora 132.8 KiB publicsuffix-list-dafsa noarch 20250116-1.fc42 fedora 68.5 KiB pyproject-srpm-macros noarch 1.18.1-1.fc43 fedora 1.9 KiB python-srpm-macros noarch 3.13-5.fc43 fedora 51.7 KiB qt5-srpm-macros noarch 5.15.16-1.fc43 fedora 500.0 B qt6-srpm-macros noarch 6.9.0-2.fc43 fedora 464.0 B readline x86_64 8.2-13.fc43 fedora 485.0 KiB rpm x86_64 5.99.90-4.fc43 fedora 3.1 MiB rpm-build-libs x86_64 5.99.90-4.fc43 fedora 264.4 KiB rpm-libs x86_64 5.99.90-4.fc43 fedora 921.5 KiB rpm-sequoia x86_64 1.8.0-1.fc43 fedora 2.5 MiB rpm-sign-libs x86_64 5.99.90-4.fc43 fedora 39.7 KiB rust-srpm-macros noarch 26.3-4.fc42 fedora 4.8 KiB setup noarch 2.15.0-23.fc43 fedora 724.7 KiB sqlite-libs x86_64 3.49.0-1.fc43 fedora 1.5 MiB systemd-libs x86_64 257.5-2.fc43 fedora 2.2 MiB systemd-standalone-sysusers x86_64 257.5-2.fc43 fedora 277.3 KiB tpm2-tss x86_64 4.1.3-7.fc43 fedora 1.6 MiB tree-sitter-srpm-macros noarch 0.2.4-1.fc43 fedora 7.5 KiB util-linux-core x86_64 2.40.4-7.fc43 fedora 1.4 MiB xxhash-libs x86_64 0.8.3-2.fc42 fedora 90.2 KiB xz-libs x86_64 1:5.8.1-1.fc43 fedora 217.8 KiB zig-srpm-macros noarch 1-4.fc42 fedora 1.1 KiB zip x86_64 3.0-43.fc42 fedora 698.5 KiB zlib-ng-compat x86_64 2.2.4-2.fc43 fedora 137.6 KiB zstd x86_64 1.5.7-1.fc43 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 161 packages Total size of inbound packages is 59 MiB. Need to download 0 B. After this operation, 198 MiB extra will be used (install 198 MiB, remove 0 B). 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Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. [ 1/163] Verify package files 100% | 1.6 KiB/s | 161.0 B | 00m00s >>> Running pre-transaction scriptlet: filesystem-0:3.18-40.fc43.x86_64 >>> Finished pre-transaction scriptlet: filesystem-0:3.18-40.fc43.x86_64 >>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1746456050.955289/root/var/cache/d [ 2/163] Prepare transaction 100% | 4.1 KiB/s | 161.0 B | 00m00s [ 3/163] Installing libgcc-0:15.1.1-1. 100% | 262.0 MiB/s | 268.3 KiB | 00m00s [ 4/163] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 5/163] Installing publicsuffix-list- 100% | 0.0 B/s | 69.2 KiB | 00m00s [ 6/163] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 7/163] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 8/163] Installing fedora-gpg-keys-0: 100% | 42.9 MiB/s | 175.9 KiB | 00m00s [ 9/163] Installing fedora-repos-0:43- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 10/163] Installing fedora-release-com 100% | 24.1 MiB/s | 24.7 KiB | 00m00s [ 11/163] Installing fedora-release-0:4 100% | 20.2 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-23.fc43.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-23.fc43.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. >>> [ 12/163] Installing setup-0:2.15.0-23. 100% | 50.9 MiB/s | 730.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/163] Installing filesystem-0:3.18- 100% | 2.7 MiB/s | 212.4 KiB | 00m00s [ 14/163] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [ 15/163] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [ 16/163] Installing pcre2-syntax-0:10. 100% | 269.9 MiB/s | 276.4 KiB | 00m00s [ 17/163] Installing ncurses-base-0:6.5 100% | 86.0 MiB/s | 352.2 KiB | 00m00s [ 18/163] Installing bash-0:5.2.37-3.fc 100% | 263.9 MiB/s | 8.2 MiB | 00m00s [ 19/163] Installing glibc-common-0:2.4 100% | 63.8 MiB/s | 1.0 MiB | 00m00s [ 20/163] Installing glibc-gconv-extra- 100% | 292.5 MiB/s | 7.3 MiB | 00m00s [ 21/163] Installing glibc-0:2.41.9000- 100% | 190.6 MiB/s | 6.7 MiB | 00m00s [ 22/163] Installing ncurses-libs-0:6.5 100% | 310.1 MiB/s | 952.8 KiB | 00m00s [ 23/163] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 24/163] Installing zlib-ng-compat-0:2 100% | 135.2 MiB/s | 138.4 KiB | 00m00s [ 25/163] Installing bzip2-libs-0:1.0.8 100% | 83.7 MiB/s | 85.7 KiB | 00m00s [ 26/163] Installing libstdc++-0:15.1.1 100% | 405.2 MiB/s | 2.8 MiB | 00m00s [ 27/163] Installing xz-libs-1:5.8.1-1. 100% | 213.8 MiB/s | 218.9 KiB | 00m00s [ 28/163] Installing gmp-1:6.3.0-3.fc43 100% | 401.1 MiB/s | 821.5 KiB | 00m00s [ 29/163] Installing libuuid-0:2.40.4-7 100% | 0.0 B/s | 38.4 KiB | 00m00s [ 30/163] Installing readline-0:8.2-13. 100% | 237.8 MiB/s | 487.1 KiB | 00m00s [ 31/163] Installing popt-0:1.19-8.fc42 100% | 68.1 MiB/s | 139.4 KiB | 00m00s [ 32/163] Installing libblkid-0:2.40.4- 100% | 257.2 MiB/s | 263.4 KiB | 00m00s [ 33/163] Installing libxcrypt-0:4.4.38 100% | 280.4 MiB/s | 287.2 KiB | 00m00s [ 34/163] Installing libzstd-0:1.5.7-1. 100% | 395.1 MiB/s | 809.1 KiB | 00m00s [ 35/163] Installing elfutils-libelf-0: 100% | 390.1 MiB/s | 1.2 MiB | 00m00s [ 36/163] Installing libgpg-error-0:1.5 100% | 60.0 MiB/s | 921.1 KiB | 00m00s [ 37/163] Installing libattr-0:2.5.2-5. 100% | 0.0 B/s | 28.1 KiB | 00m00s [ 38/163] Installing libacl-0:2.3.2-3.f 100% | 0.0 B/s | 39.2 KiB | 00m00s [ 39/163] Installing libtasn1-0:4.20.0- 100% | 173.9 MiB/s | 178.1 KiB | 00m00s [ 40/163] Installing libunistring-0:1.1 100% | 345.3 MiB/s | 1.7 MiB | 00m00s [ 41/163] Installing libidn2-0:2.3.8-1. 100% | 68.2 MiB/s | 558.7 KiB | 00m00s [ 42/163] Installing crypto-policies-0: 100% | 40.7 MiB/s | 166.6 KiB | 00m00s [ 43/163] Installing dwz-0:0.15-9.fc42. 100% | 20.4 MiB/s | 292.4 KiB | 00m00s [ 44/163] Installing mpfr-0:4.2.2-1.fc4 100% | 270.3 MiB/s | 830.4 KiB | 00m00s [ 45/163] Installing gawk-0:5.3.2-1.fc4 100% | 100.9 MiB/s | 1.8 MiB | 00m00s [ 46/163] Installing unzip-0:6.0-66.fc4 100% | 29.6 MiB/s | 393.8 KiB | 00m00s [ 47/163] Installing file-libs-0:5.46-1 100% | 697.5 MiB/s | 11.9 MiB | 00m00s [ 48/163] Installing file-0:5.46-1.fc42 100% | 8.3 MiB/s | 101.7 KiB | 00m00s [ 49/163] Installing pcre2-0:10.45-1.fc 100% | 341.4 MiB/s | 699.1 KiB | 00m00s [ 50/163] Installing grep-0:3.12-1.fc43 100% | 62.7 MiB/s | 1.0 MiB | 00m00s [ 51/163] Installing xz-1:5.8.1-1.fc43. 100% | 78.3 MiB/s | 1.3 MiB | 00m00s [ 52/163] Installing libeconf-0:0.7.6-1 100% | 64.7 MiB/s | 66.2 KiB | 00m00s [ 53/163] Installing libcap-ng-0:0.8.5- 100% | 73.1 MiB/s | 74.8 KiB | 00m00s [ 54/163] Installing audit-libs-0:4.0.3 100% | 345.1 MiB/s | 353.4 KiB | 00m00s [ 55/163] Installing pam-libs-0:1.7.0-4 100% | 126.1 MiB/s | 129.1 KiB | 00m00s [ 56/163] Installing libcap-0:2.76-1.fc 100% | 16.1 MiB/s | 214.3 KiB | 00m00s [ 57/163] Installing systemd-libs-0:257 100% | 371.3 MiB/s | 2.2 MiB | 00m00s [ 58/163] Installing libsmartcols-0:2.4 100% | 177.3 MiB/s | 181.5 KiB | 00m00s [ 59/163] Installing libsepol-0:3.8-1.f 100% | 403.8 MiB/s | 827.0 KiB | 00m00s [ 60/163] Installing libselinux-0:3.8-1 100% | 189.8 MiB/s | 194.3 KiB | 00m00s [ 61/163] Installing sed-0:4.9-4.fc42.x 100% | 56.3 MiB/s | 865.5 KiB | 00m00s [ 62/163] Installing findutils-1:4.10.0 100% | 110.2 MiB/s | 1.9 MiB | 00m00s [ 63/163] Installing libmount-0:2.40.4- 100% | 349.0 MiB/s | 357.4 KiB | 00m00s [ 64/163] Installing lz4-libs-0:1.10.0- 100% | 154.7 MiB/s | 158.5 KiB | 00m00s [ 65/163] Installing lua-libs-0:5.4.7-3 100% | 271.5 MiB/s | 278.1 KiB | 00m00s [ 66/163] Installing sqlite-libs-0:3.49 100% | 381.0 MiB/s | 1.5 MiB | 00m00s [ 67/163] Installing json-c-0:0.18-2.fc 100% | 0.0 B/s | 88.0 KiB | 00m00s [ 68/163] Installing libffi-0:3.4.7-4.f 100% | 82.0 MiB/s | 84.0 KiB | 00m00s [ 69/163] Installing p11-kit-0:0.25.5-5 100% | 115.0 MiB/s | 2.2 MiB | 00m00s [ 70/163] Installing alternatives-0:1.3 100% | 5.2 MiB/s | 63.8 KiB | 00m00s [ 71/163] Installing p11-kit-trust-0:0. 100% | 20.4 MiB/s | 397.2 KiB | 00m00s [ 72/163] Installing zstd-0:1.5.7-1.fc4 100% | 106.9 MiB/s | 1.7 MiB | 00m00s [ 73/163] Installing util-linux-core-0: 100% | 79.3 MiB/s | 1.4 MiB | 00m00s [ 74/163] Installing tar-2:1.35-5.fc42. 100% | 155.9 MiB/s | 3.0 MiB | 00m00s [ 75/163] Installing libsemanage-0:3.8- 100% | 302.9 MiB/s | 310.2 KiB | 00m00s [ 76/163] Installing systemd-standalone 100% | 22.6 MiB/s | 277.9 KiB | 00m00s [ 77/163] Installing libusb1-0:1.0.28-2 100% | 168.7 MiB/s | 172.7 KiB | 00m00s [ 78/163] Installing zip-0:3.0-43.fc42. 100% | 52.8 MiB/s | 702.4 KiB | 00m00s [ 79/163] Installing libpsl-0:0.21.5-5. 100% | 75.7 MiB/s | 77.5 KiB | 00m00s [ 80/163] Installing libassuan-0:2.5.7- 100% | 165.6 MiB/s | 169.6 KiB | 00m00s [ 81/163] Installing libgcrypt-0:1.11.0 100% | 392.3 MiB/s | 1.6 MiB | 00m00s [ 82/163] Installing libksba-0:1.6.7-3. 100% | 395.6 MiB/s | 405.1 KiB | 00m00s [ 83/163] Installing libfdisk-0:2.40.4- 100% | 364.7 MiB/s | 373.5 KiB | 00m00s [ 84/163] Installing nettle-0:3.10.1-1. 100% | 387.5 MiB/s | 793.6 KiB | 00m00s [ 85/163] Installing gnutls-0:3.8.9-5.f 100% | 397.1 MiB/s | 3.6 MiB | 00m00s [ 86/163] Installing libxml2-0:2.12.10- 100% | 106.0 MiB/s | 1.7 MiB | 00m00s [ 87/163] Installing bzip2-0:1.0.8-20.f 100% | 8.5 MiB/s | 103.8 KiB | 00m00s [ 88/163] Installing add-determinism-0: 100% | 145.1 MiB/s | 2.5 MiB | 00m00s [ 89/163] Installing build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s [ 90/163] Installing cpio-0:2.15-2.fc41 100% | 73.3 MiB/s | 1.1 MiB | 00m00s [ 91/163] Installing diffutils-0:3.12-1 100% | 97.6 MiB/s | 1.6 MiB | 00m00s [ 92/163] Installing ed-0:1.21-2.fc42.x 100% | 12.1 MiB/s | 148.8 KiB | 00m00s [ 93/163] Installing patch-0:2.8-1.fc43 100% | 18.6 MiB/s | 228.3 KiB | 00m00s [ 94/163] Installing libgomp-0:15.1.1-1 100% | 263.6 MiB/s | 539.9 KiB | 00m00s [ 95/163] Installing npth-0:1.8-2.fc42. 100% | 0.0 B/s | 50.7 KiB | 00m00s [ 96/163] Installing libtool-ltdl-0:2.5 100% | 0.0 B/s | 71.2 KiB | 00m00s [ 97/163] Installing gdbm-libs-1:1.23-9 100% | 128.5 MiB/s | 131.6 KiB | 00m00s [ 98/163] Installing cyrus-sasl-lib-0:2 100% | 135.5 MiB/s | 2.3 MiB | 00m00s [ 99/163] Installing jansson-0:2.14-2.f 100% | 92.2 MiB/s | 94.4 KiB | 00m00s [100/163] Installing libpkgconf-0:2.3.0 100% | 0.0 B/s | 79.2 KiB | 00m00s [101/163] Installing pkgconf-0:2.3.0-2. 100% | 7.4 MiB/s | 91.0 KiB | 00m00s [102/163] Installing pkgconf-pkg-config 100% | 161.2 KiB/s | 1.8 KiB | 00m00s [103/163] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [104/163] Installing libbrotli-0:1.1.0- 100% | 274.6 MiB/s | 843.6 KiB | 00m00s [105/163] Installing libnghttp2-0:1.65. 100% | 159.5 MiB/s | 163.3 KiB | 00m00s [106/163] Installing keyutils-libs-0:1. 100% | 0.0 B/s | 59.7 KiB | 00m00s [107/163] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 68.2 KiB | 00m00s [108/163] Installing libverto-0:0.3.2-1 100% | 0.0 B/s | 27.2 KiB | 00m00s [109/163] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [110/163] Installing elfutils-default-y 100% | 510.7 KiB/s | 2.0 KiB | 00m00s [111/163] Installing elfutils-libs-0:0. 100% | 220.3 MiB/s | 676.7 KiB | 00m00s [112/163] Installing coreutils-common-0 100% | 403.3 MiB/s | 11.3 MiB | 00m00s [113/163] Installing openssl-libs-1:3.5 100% | 423.3 MiB/s | 8.9 MiB | 00m00s [114/163] Installing coreutils-0:9.7-1. 100% | 170.1 MiB/s | 5.4 MiB | 00m00s [115/163] Installing ca-certificates-0: 100% | 2.1 MiB/s | 2.4 MiB | 00m01s [116/163] Installing libarchive-0:3.7.7 100% | 303.6 MiB/s | 932.6 KiB | 00m00s [117/163] Installing krb5-libs-0:1.21.3 100% | 176.9 MiB/s | 2.3 MiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-7.fc43.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-7.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [118/163] Installing tpm2-tss-0:4.1.3-7 100% | 261.3 MiB/s | 1.6 MiB | 00m00s [119/163] Installing ima-evm-utils-libs 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [120/163] Installing libssh-0:0.11.1-4. 100% | 277.1 MiB/s | 567.5 KiB | 00m00s [121/163] Installing gzip-0:1.13-3.fc42 100% | 25.9 MiB/s | 398.4 KiB | 00m00s [122/163] Installing rpm-sequoia-0:1.8. 100% | 357.7 MiB/s | 2.5 MiB | 00m00s [123/163] Installing rpm-libs-0:5.99.90 100% | 300.5 MiB/s | 923.1 KiB | 00m00s [124/163] Installing libfsverity-0:1.6- 100% | 0.0 B/s | 33.5 KiB | 00m00s [125/163] Installing libevent-0:2.1.12- 100% | 295.2 MiB/s | 906.9 KiB | 00m00s [126/163] Installing openldap-0:2.6.9-5 100% | 321.7 MiB/s | 658.9 KiB | 00m00s [127/163] Installing libcurl-0:8.14.0~r 100% | 290.4 MiB/s | 892.1 KiB | 00m00s [128/163] Installing elfutils-debuginfo 100% | 6.5 MiB/s | 86.2 KiB | 00m00s [129/163] Installing elfutils-0:0.192-8 100% | 149.3 MiB/s | 2.7 MiB | 00m00s [130/163] Installing binutils-0:2.44-3. 100% | 340.8 MiB/s | 25.9 MiB | 00m00s [131/163] Installing gdb-minimal-0:16.3 100% | 288.0 MiB/s | 13.2 MiB | 00m00s [132/163] Installing debugedit-0:5.1-6. 100% | 15.9 MiB/s | 195.4 KiB | 00m00s [133/163] Installing curl-0:8.14.0~rc1- 100% | 23.2 MiB/s | 476.0 KiB | 00m00s [134/163] Installing rpm-0:5.99.90-4.fc 100% | 80.9 MiB/s | 2.5 MiB | 00m00s [135/163] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.1 KiB | 00m00s [136/163] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [137/163] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 8.6 KiB | 00m00s [138/163] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [139/163] Installing gnupg2-0:2.4.7-3.f 100% | 251.1 MiB/s | 9.8 MiB | 00m00s [140/163] Installing rpm-sign-libs-0:5. 100% | 39.6 MiB/s | 40.5 KiB | 00m00s [141/163] Installing rpm-build-libs-0:5 100% | 259.0 MiB/s | 265.2 KiB | 00m00s [142/163] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [143/163] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 740.0 B | 00m00s [144/163] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [145/163] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [146/163] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [147/163] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [148/163] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [149/163] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [150/163] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [151/163] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [152/163] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [153/163] Installing rpm-build-0:5.99.9 100% | 20.3 MiB/s | 290.5 KiB | 00m00s [154/163] Installing pyproject-srpm-mac 100% | 0.0 B/s | 2.5 KiB | 00m00s [155/163] Installing redhat-rpm-config- 100% | 93.9 MiB/s | 192.3 KiB | 00m00s [156/163] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [157/163] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [158/163] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 62.0 KiB | 00m00s [159/163] Installing python-srpm-macros 100% | 0.0 B/s | 53.0 KiB | 00m00s [160/163] Installing which-0:2.23-1.fc4 100% | 6.0 MiB/s | 85.6 KiB | 00m00s [161/163] Installing util-linux-0:2.40. 100% | 101.8 MiB/s | 3.5 MiB | 00m00s [162/163] Installing shadow-utils-2:4.1 100% | 135.1 MiB/s | 4.1 MiB | 00m00s [163/163] Installing info-0:7.2-3.fc42. 100% | 235.4 KiB/s | 358.3 KiB | 00m02s Warning: skipped OpenPGP checks for 1 package from repository: copr_base Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.6.0-1.fc43.x86_64 alternatives-1.32-1.fc43.x86_64 ansible-srpm-macros-1-17.1.fc42.noarch audit-libs-4.0.3-2.fc42.x86_64 bash-5.2.37-3.fc43.x86_64 binutils-2.44-3.fc43.x86_64 build-reproducibility-srpm-macros-0.6.0-1.fc43.noarch bzip2-1.0.8-20.fc42.x86_64 bzip2-libs-1.0.8-20.fc42.x86_64 ca-certificates-2024.2.69_v8.0.401-5.fc42.noarch coreutils-9.7-1.fc43.x86_64 coreutils-common-9.7-1.fc43.x86_64 cpio-2.15-2.fc41.x86_64 crypto-policies-20250402-2.git86c0178.fc43.noarch curl-8.14.0~rc1-1.fc43.x86_64 cyrus-sasl-lib-2.1.28-30.fc42.x86_64 debugedit-5.1-6.fc43.x86_64 diffutils-3.12-1.fc43.x86_64 dwz-0.15-9.fc42.x86_64 ed-1.21-2.fc42.x86_64 efi-srpm-macros-6-3.fc43.noarch elfutils-0.192-8.fc42.x86_64 elfutils-debuginfod-client-0.192-8.fc42.x86_64 elfutils-default-yama-scope-0.192-8.fc42.noarch elfutils-libelf-0.192-8.fc42.x86_64 elfutils-libs-0.192-8.fc42.x86_64 fedora-gpg-keys-43-0.2.noarch fedora-release-43-0.15.noarch fedora-release-common-43-0.15.noarch fedora-release-identity-basic-43-0.15.noarch fedora-repos-43-0.2.noarch fedora-repos-rawhide-43-0.2.noarch file-5.46-1.fc42.x86_64 file-libs-5.46-1.fc42.x86_64 filesystem-3.18-40.fc43.x86_64 filesystem-srpm-macros-3.18-40.fc43.noarch findutils-4.10.0-5.fc42.x86_64 fonts-srpm-macros-2.0.5-21.fc42.noarch forge-srpm-macros-0.4.0-2.fc42.noarch fpc-srpm-macros-1.3-14.fc42.noarch gawk-5.3.2-1.fc43.x86_64 gdb-minimal-16.3-1.fc43.x86_64 gdbm-libs-1.23-9.fc42.x86_64 ghc-srpm-macros-1.9.2-2.fc42.noarch glibc-2.41.9000-12.fc43.x86_64 glibc-common-2.41.9000-12.fc43.x86_64 glibc-gconv-extra-2.41.9000-12.fc43.x86_64 glibc-minimal-langpack-2.41.9000-12.fc43.x86_64 gmp-6.3.0-3.fc43.x86_64 gnat-srpm-macros-6-7.fc42.noarch gnupg2-2.4.7-3.fc43.x86_64 gnutls-3.8.9-5.fc43.x86_64 go-srpm-macros-3.6.0-7.fc43.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-b0f4950458f69e1150c6c5edc8ac4916105ef944-65ca83d1 gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf grep-3.12-1.fc43.x86_64 gzip-1.13-3.fc42.x86_64 ima-evm-utils-libs-1.6.2-5.fc43.x86_64 info-7.2-3.fc42.x86_64 jansson-2.14-2.fc42.x86_64 json-c-0.18-2.fc42.x86_64 kernel-srpm-macros-1.0-25.fc42.noarch keyutils-libs-1.6.3-5.fc42.x86_64 krb5-libs-1.21.3-5.fc42.x86_64 libacl-2.3.2-3.fc42.x86_64 libarchive-3.7.7-4.fc43.x86_64 libassuan-2.5.7-3.fc42.x86_64 libattr-2.5.2-5.fc42.x86_64 libblkid-2.40.4-7.fc43.x86_64 libbrotli-1.1.0-6.fc42.x86_64 libcap-2.76-1.fc43.x86_64 libcap-ng-0.8.5-4.fc42.x86_64 libcom_err-1.47.2-3.fc42.x86_64 libcurl-8.14.0~rc1-1.fc43.x86_64 libeconf-0.7.6-1.fc43.x86_64 libevent-2.1.12-15.fc42.x86_64 libfdisk-2.40.4-7.fc43.x86_64 libffi-3.4.7-4.fc43.x86_64 libfsverity-1.6-2.fc42.x86_64 libgcc-15.1.1-1.fc43.x86_64 libgcrypt-1.11.0-5.fc42.x86_64 libgomp-15.1.1-1.fc43.x86_64 libgpg-error-1.55-1.fc43.x86_64 libidn2-2.3.8-1.fc43.x86_64 libksba-1.6.7-3.fc42.x86_64 libmount-2.40.4-7.fc43.x86_64 libnghttp2-1.65.0-1.fc43.x86_64 libpkgconf-2.3.0-2.fc42.x86_64 libpsl-0.21.5-5.fc42.x86_64 libselinux-3.8-1.fc42.x86_64 libsemanage-3.8-1.fc42.x86_64 libsepol-3.8-1.fc42.x86_64 libsmartcols-2.40.4-7.fc43.x86_64 libssh-0.11.1-4.fc42.x86_64 libssh-config-0.11.1-4.fc42.noarch libstdc++-15.1.1-1.fc43.x86_64 libtasn1-4.20.0-1.fc43.x86_64 libtool-ltdl-2.5.4-4.fc42.x86_64 libunistring-1.1-9.fc42.x86_64 libusb1-1.0.28-2.fc43.x86_64 libuuid-2.40.4-7.fc43.x86_64 libverto-0.3.2-10.fc42.x86_64 libxcrypt-4.4.38-7.fc43.x86_64 libxml2-2.12.10-1.fc43.x86_64 libzstd-1.5.7-1.fc43.x86_64 lua-libs-5.4.7-3.fc43.x86_64 lua-srpm-macros-1-15.fc42.noarch lz4-libs-1.10.0-2.fc42.x86_64 mpfr-4.2.2-1.fc43.x86_64 ncurses-base-6.5-5.20250125.fc42.noarch ncurses-libs-6.5-5.20250125.fc42.x86_64 nettle-3.10.1-1.fc43.x86_64 npth-1.8-2.fc42.x86_64 ocaml-srpm-macros-10-4.fc42.noarch openblas-srpm-macros-2-19.fc42.noarch openldap-2.6.9-5.fc43.x86_64 openssl-libs-3.5.0-3.fc43.x86_64 p11-kit-0.25.5-5.fc42.x86_64 p11-kit-trust-0.25.5-5.fc42.x86_64 package-notes-srpm-macros-0.5-13.fc42.noarch pam-libs-1.7.0-4.fc42.x86_64 patch-2.8-1.fc43.x86_64 pcre2-10.45-1.fc43.x86_64 pcre2-syntax-10.45-1.fc43.noarch perl-srpm-macros-1-58.fc43.noarch pkgconf-2.3.0-2.fc42.x86_64 pkgconf-m4-2.3.0-2.fc42.noarch pkgconf-pkg-config-2.3.0-2.fc42.x86_64 popt-1.19-8.fc42.x86_64 publicsuffix-list-dafsa-20250116-1.fc42.noarch pyproject-srpm-macros-1.18.1-1.fc43.noarch python-srpm-macros-3.13-5.fc43.noarch qt5-srpm-macros-5.15.16-1.fc43.noarch qt6-srpm-macros-6.9.0-2.fc43.noarch readline-8.2-13.fc43.x86_64 redhat-rpm-config-343-4.fc43.noarch rpm-5.99.90-4.fc43.x86_64 rpm-build-5.99.90-4.fc43.x86_64 rpm-build-libs-5.99.90-4.fc43.x86_64 rpm-libs-5.99.90-4.fc43.x86_64 rpm-sequoia-1.8.0-1.fc43.x86_64 rpm-sign-libs-5.99.90-4.fc43.x86_64 rust-srpm-macros-26.3-4.fc42.noarch sed-4.9-4.fc42.x86_64 setup-2.15.0-23.fc43.noarch shadow-utils-4.17.4-1.fc43.x86_64 sqlite-libs-3.49.0-1.fc43.x86_64 systemd-libs-257.5-2.fc43.x86_64 systemd-standalone-sysusers-257.5-2.fc43.x86_64 tar-1.35-5.fc42.x86_64 tpm2-tss-4.1.3-7.fc43.x86_64 tree-sitter-srpm-macros-0.2.4-1.fc43.noarch unzip-6.0-66.fc42.x86_64 util-linux-2.40.4-7.fc43.x86_64 util-linux-core-2.40.4-7.fc43.x86_64 which-2.23-1.fc42.x86_64 xxhash-libs-0.8.3-2.fc42.x86_64 xz-5.8.1-1.fc43.x86_64 xz-libs-5.8.1-1.fc43.x86_64 zig-srpm-macros-1-4.fc42.noarch zip-3.0-43.fc42.x86_64 zlib-ng-compat-2.2.4-2.fc43.x86_64 zstd-1.5.7-1.fc43.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1745452800 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-13.fc43.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1746456050.955289/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-b5aj_zzz/bcftools/bcftools.spec) Config(child) 0 minutes 10 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/bcftools-1.15.1-13.fc43.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1746456050.955289/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1746456050.955289/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1746456050.955289/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-5.99.90-4.fc43.x86_64 rpm-sequoia-1.8.0-1.fc43.x86_64 dnf5-5.2.13.1-1.fc43.x86_64 dnf5-plugins-5.2.13.1-1.fc43.x86_64 Finish: chroot init Start: build phase for bcftools-1.15.1-13.fc43.src.rpm Start: build setup for bcftools-1.15.1-13.fc43.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1745452800 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-13.fc43.src.rpm Updating and loading repositories: fedora 100% | 71.6 KiB/s | 25.9 KiB | 00m00s Copr repository 100% | 89.9 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 1.6 MiB/s | 127.8 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc x86_64 15.1.1-1.fc43 fedora 111.0 MiB gsl-devel x86_64 2.8-1.fc42 fedora 1.6 MiB htslib-devel x86_64 1.15.1-8.fc42 fedora 411.0 KiB htslib-tools x86_64 1.15.1-8.fc42 fedora 2.4 MiB make x86_64 1:4.4.1-10.fc42 fedora 1.8 MiB perl-ExtUtils-Embed noarch 1.35-518.fc43 copr_base 15.6 KiB perl-File-Temp noarch 1:0.231.100-518.fc43 copr_base 127.6 KiB perl-FindBin noarch 1.54-518.fc43 copr_base 6.8 KiB perl-Getopt-Long noarch 1:2.58-518.fc43 copr_base 101.6 KiB perl-interpreter x86_64 4:5.41.12-518.fc43 copr_base 119.2 KiB zlib-ng-compat-devel x86_64 2.2.4-2.fc43 fedora 107.0 KiB Installing dependencies: annobin-docs noarch 12.93-1.fc43 fedora 98.9 KiB annobin-plugin-gcc x86_64 12.93-1.fc43 fedora 993.4 KiB cmake-filesystem x86_64 3.31.6-2.fc43 fedora 0.0 B cpp x86_64 15.1.1-1.fc43 fedora 37.8 MiB expat x86_64 2.7.1-1.fc43 fedora 294.2 KiB gcc-plugin-annobin x86_64 15.1.1-1.fc43 fedora 57.2 KiB glibc-devel x86_64 2.41.9000-12.fc43 fedora 2.3 MiB groff-base x86_64 1.23.0-8.fc42 fedora 3.9 MiB gsl x86_64 2.8-1.fc42 fedora 3.5 MiB htslib x86_64 1.15.1-8.fc42 fedora 1.1 MiB kernel-headers x86_64 6.15.0-0.rc4.35.fc43 fedora 6.6 MiB libb2 x86_64 0.98.1-13.fc42 fedora 46.1 KiB libmpc x86_64 1.3.1-7.fc42 fedora 164.5 KiB libxcrypt-devel x86_64 4.4.38-7.fc43 fedora 30.8 KiB mpdecimal x86_64 4.0.0-2.fc43 fedora 216.8 KiB ncurses x86_64 6.5-5.20250125.fc42 fedora 608.1 KiB perl-AutoSplit noarch 5.74-518.fc43 copr_base 23.1 KiB perl-B x86_64 1.89-518.fc43 copr_base 501.3 KiB perl-Benchmark noarch 1.27-518.fc43 copr_base 36.4 KiB perl-Carp noarch 1.54-518.fc43 copr_base 41.1 KiB perl-Class-Struct noarch 0.68-518.fc43 copr_base 25.4 KiB perl-Data-Dumper x86_64 2.192-518.fc43 copr_base 100.8 KiB perl-Devel-PPPort x86_64 3.73-518.fc43 copr_base 643.6 KiB perl-DynaLoader x86_64 1.57-518.fc43 copr_base 32.1 KiB perl-Encode x86_64 4:3.21-518.fc43 copr_base 4.6 MiB perl-Errno x86_64 1.38-518.fc43 copr_base 8.4 KiB perl-Exporter noarch 5.79-519.fc43 copr_base 54.3 KiB perl-ExtUtils-Command noarch 2:7.74-518.fc43 copr_base 9.6 KiB perl-ExtUtils-Constant noarch 0.25-518.fc43 copr_base 85.9 KiB perl-ExtUtils-Install noarch 2.22-518.fc43 copr_base 72.3 KiB perl-ExtUtils-MakeMaker noarch 2:7.74-518.fc43 copr_base 614.1 KiB perl-ExtUtils-Manifest noarch 1:1.75-518.fc43 copr_base 28.2 KiB perl-ExtUtils-ParseXS noarch 1:3.57-518.fc43 copr_base 462.0 KiB perl-Fcntl x86_64 1.20-518.fc43 copr_base 48.8 KiB perl-File-Basename noarch 2.86-518.fc43 copr_base 14.0 KiB perl-File-Compare noarch 1.100.800-518.fc43 copr_base 5.6 KiB perl-File-Copy noarch 2.41-518.fc43 copr_base 19.7 KiB perl-File-Find noarch 1.44-518.fc43 copr_base 42.0 KiB perl-File-Path noarch 2.18-518.fc43 copr_base 51.5 KiB perl-File-stat noarch 1.14-518.fc43 copr_base 12.5 KiB perl-Getopt-Std noarch 1.14-518.fc43 copr_base 11.2 KiB perl-HTTP-Tiny noarch 0.090-518.fc43 copr_base 88.7 KiB perl-Hash-Util x86_64 0.32-518.fc43 copr_base 55.0 KiB perl-Hash-Util-FieldHash x86_64 1.27-518.fc43 copr_base 62.6 KiB perl-IO x86_64 1.55-518.fc43 copr_base 147.4 KiB perl-IPC-Open3 noarch 1.24-518.fc43 copr_base 27.7 KiB perl-MIME-Base64 x86_64 3.16-518.fc43 copr_base 28.9 KiB perl-POSIX x86_64 2.23-518.fc43 copr_base 231.4 KiB perl-PathTools x86_64 3.94-519.fc43 copr_base 180.0 KiB perl-Pod-Escapes noarch 1:1.07-518.fc43 copr_base 20.7 KiB perl-Pod-Perldoc noarch 3.28.01-518.fc43 copr_base 139.8 KiB perl-Pod-Simple noarch 1:3.45-518.fc43 copr_base 522.3 KiB perl-Pod-Usage noarch 4:2.05-518.fc43 copr_base 43.2 KiB perl-Scalar-List-Utils x86_64 5:1.69-518.fc43 copr_base 121.4 KiB perl-SelectSaver noarch 1.02-518.fc43 copr_base 2.2 KiB perl-Socket x86_64 4:2.038-518.fc43 copr_base 89.4 KiB perl-Storable x86_64 1:3.37-519.fc43 copr_base 231.2 KiB perl-Symbol noarch 1.09-518.fc43 copr_base 6.8 KiB perl-Term-ANSIColor noarch 5.01-518.fc43 copr_base 66.8 KiB perl-Term-Cap noarch 1.18-518.fc43 copr_base 23.0 KiB perl-Test-Harness noarch 1:3.50-518.fc43 copr_base 460.5 KiB perl-Text-ParseWords noarch 3.31-518.fc43 copr_base 10.7 KiB perl-Text-Tabs+Wrap noarch 2024.001-518.fc43 copr_base 17.4 KiB perl-Time-Local noarch 2:1.350-518.fc43 copr_base 22.0 KiB perl-base noarch 2.27-518.fc43 copr_base 12.6 KiB perl-constant noarch 1.33-518.fc43 copr_base 19.2 KiB perl-devel x86_64 4:5.41.12-518.fc43 copr_base 3.8 MiB perl-fields noarch 2.27-518.fc43 copr_base 11.9 KiB perl-if noarch 0.61.000-518.fc43 copr_base 5.8 KiB perl-lib x86_64 0.65-518.fc43 copr_base 8.5 KiB perl-libs x86_64 4:5.41.12-518.fc43 copr_base 11.5 MiB perl-locale noarch 1.13-518.fc43 copr_base 6.1 KiB perl-mro x86_64 1.29-518.fc43 copr_base 41.6 KiB perl-overload noarch 1.40-518.fc43 copr_base 71.6 KiB perl-overloading noarch 0.02-518.fc43 copr_base 4.9 KiB perl-parent noarch 1:0.244-518.fc43 copr_base 4.6 KiB perl-podlators noarch 1:6.0.2-518.fc43 copr_base 255.3 KiB perl-vars noarch 1.05-518.fc43 copr_base 3.9 KiB perl-version noarch 9:0.99.33-518.fc43 copr_base 53.4 KiB python-pip-wheel noarch 25.1.1-1.fc43 fedora 1.2 MiB python3 x86_64 3.13.3-2.fc43 fedora 28.7 KiB python3-libs x86_64 3.13.3-2.fc43 fedora 39.9 MiB python3-pyparsing noarch 3.1.2-8.fc42 fedora 996.4 KiB systemtap-sdt-devel x86_64 5.3-1.fc43 fedora 182.9 KiB systemtap-sdt-dtrace x86_64 5.3-1.fc43 fedora 179.6 KiB tzdata noarch 2025b-1.fc43 fedora 1.6 MiB Transaction Summary: Installing: 97 packages Total size of inbound packages is 80 MiB. Need to download 3 MiB. After this operation, 245 MiB extra will be used (install 245 MiB, remove 0 B). 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Finish: build setup for bcftools-1.15.1-13.fc43.src.rpm Start: rpmbuild bcftools-1.15.1-13.fc43.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1745452800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.kCwgc8 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.mp5Gwb + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd /builddir/build/BUILD/bcftools-1.15.1-build + rm -rf bcftools-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bcftools-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch):' Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file plugins/fill-tags.c + sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats + sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.rAQL4T + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure --- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./htslib-1.15.1/configure 2025-05-05 14:41:08.659491750 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for x86_64-redhat-linux-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes checking for library containing Perl_call_pv... -lperl checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ + /usr/bin/make -O -j4 V=1 VERBOSE=1 echo '#define BCFTOOLS_VERSION "1.15.1"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfindex.o vcfindex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfisec.o vcfisec.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfquery.o vcfquery.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcffilter.o vcffilter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfstats.o vcfstats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfsom.o vcfsom.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfview.o vcfview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfmerge.o vcfmerge.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfnorm.o vcfnorm.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfroh.o vcfroh.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o gvcf.o gvcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfcall.o vcfcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o mcall.o mcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o reheader.o reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfhead.o vcfhead.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o HMM.o HMM.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o ploidy.o ploidy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o convert.o convert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bin.o bin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o version.o version.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o hclust.o hclust.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o consensus.o consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o mpileup.o mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o cols.o cols.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o vcfsort.o vcfsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o bam_sample.o bam_sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o dist.o dist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o extsort.o extsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o ccall.o ccall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe 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-c -o abuf.o abuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o prob1.o prob1.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o peakfit.o peakfit.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o polysomy.o polysomy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o test/test-rbuf.o test/test-rbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -c -o csq.o csq.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -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 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ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/mendelian.so version.c plugins/mendelian.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -DUSE_GPL -c -o main.o main.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-rbuf test/test-rbuf.o -lz gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.cjdjR3 + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + '[' /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build + mkdir /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /usr/bin/install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/libexec/bcftools + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.15.1-13.fc43 --unique-debug-suffix -1.15.1-13.fc43.x86_64 --unique-debug-src-base bcftools-1.15.1-13.fc43.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1 find-debuginfo: starting Extracting debug info from 39 files DWARF-compressing 39 files sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bcftools-1.15.1-13.fc43.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /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-determinism --brp -j4 /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT Scanned 19 directories and 208 files, processed 1 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/bcftools-1.15.1-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.fZNSmQ + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x00007f485db70000) + make test ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools ./test/test.pl: module IO::Pty not found; skipping usage tests test_tabix: tabix /tmp/KeutieM3kJ/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/KeutieM3kJ/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H /tmp/KeutieM3kJ/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/KeutieM3kJ/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/KeutieM3kJ/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/KeutieM3kJ/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/KeutieM3kJ/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/KeutieM3kJ/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -s /tmp/KeutieM3kJ/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools index -n /tmp/KeutieM3kJ/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/KeutieM3kJ/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/misc/plot-vcfstats -m /tmp/KeutieM3kJ/check.1.chk /tmp/KeutieM3kJ/check.2.chk /tmp/KeutieM3kJ/check.3.chk /tmp/KeutieM3kJ/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/KeutieM3kJ/stats.a.vcf.gz /tmp/KeutieM3kJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s B /tmp/KeutieM3kJ/stats.a.vcf.gz /tmp/KeutieM3kJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools stats -s - /tmp/KeutieM3kJ/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -c both /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -c both /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n =2 -c any /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n =2 -c any /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -C -c any /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -C -c any /tmp/KeutieM3kJ/isec.a.vcf.gz /tmp/KeutieM3kJ/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec --no-version -T /tmp/KeutieM3kJ/isec.tab.gz /tmp/KeutieM3kJ/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -T /tmp/KeutieM3kJ/isec.tab.gz /tmp/KeutieM3kJ/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/KeutieM3kJ/isec-miss.1.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/KeutieM3kJ/isec-miss.1.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/KeutieM3kJ/isec-miss.1.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/KeutieM3kJ/isec-miss.1.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/KeutieM3kJ/isec-miss.2.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/KeutieM3kJ/isec-miss.2.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/KeutieM3kJ/isec-miss.2.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/KeutieM3kJ/isec-miss.2.1.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.2.vcf.gz /tmp/KeutieM3kJ/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/KeutieM3kJ/merge.join.a.vcf.gz /tmp/KeutieM3kJ/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/KeutieM3kJ/merge.join.a.vcf.gz /tmp/KeutieM3kJ/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/KeutieM3kJ/merge.join.a.bcf /tmp/KeutieM3kJ/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/KeutieM3kJ/merge.join.a.bcf /tmp/KeutieM3kJ/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/KeutieM3kJ/merge.LPL.a.vcf.gz /tmp/KeutieM3kJ/merge.LPL.b.vcf.gz /tmp/KeutieM3kJ/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/KeutieM3kJ/merge.LPL.a.bcf /tmp/KeutieM3kJ/merge.LPL.b.bcf /tmp/KeutieM3kJ/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/KeutieM3kJ/merge.a.vcf.gz /tmp/KeutieM3kJ/merge.b.vcf.gz /tmp/KeutieM3kJ/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/KeutieM3kJ/merge.a.vcf.gz /tmp/KeutieM3kJ/merge.b.vcf.gz /tmp/KeutieM3kJ/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/KeutieM3kJ/merge.a.bcf /tmp/KeutieM3kJ/merge.b.bcf /tmp/KeutieM3kJ/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/KeutieM3kJ/merge.a.bcf /tmp/KeutieM3kJ/merge.b.bcf /tmp/KeutieM3kJ/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/KeutieM3kJ/merge.a.vcf.gz /tmp/KeutieM3kJ/merge.b.vcf.gz /tmp/KeutieM3kJ/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/KeutieM3kJ/merge.a.vcf.gz /tmp/KeutieM3kJ/merge.b.vcf.gz /tmp/KeutieM3kJ/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/KeutieM3kJ/merge.a.bcf /tmp/KeutieM3kJ/merge.b.bcf /tmp/KeutieM3kJ/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/KeutieM3kJ/merge.a.bcf /tmp/KeutieM3kJ/merge.b.bcf /tmp/KeutieM3kJ/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/KeutieM3kJ/merge.a.vcf.gz /tmp/KeutieM3kJ/merge.b.vcf.gz /tmp/KeutieM3kJ/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/KeutieM3kJ/merge.a.vcf.gz /tmp/KeutieM3kJ/merge.b.vcf.gz /tmp/KeutieM3kJ/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/KeutieM3kJ/merge.a.bcf /tmp/KeutieM3kJ/merge.b.bcf /tmp/KeutieM3kJ/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/KeutieM3kJ/merge.a.bcf /tmp/KeutieM3kJ/merge.b.bcf /tmp/KeutieM3kJ/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/KeutieM3kJ/merge.2.a.vcf.gz /tmp/KeutieM3kJ/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/KeutieM3kJ/merge.2.a.vcf.gz /tmp/KeutieM3kJ/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/KeutieM3kJ/merge.2.a.bcf /tmp/KeutieM3kJ/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/KeutieM3kJ/merge.2.a.bcf /tmp/KeutieM3kJ/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/KeutieM3kJ/merge.2.a.vcf.gz /tmp/KeutieM3kJ/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/KeutieM3kJ/merge.2.a.vcf.gz /tmp/KeutieM3kJ/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/KeutieM3kJ/merge.2.a.bcf /tmp/KeutieM3kJ/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/KeutieM3kJ/merge.2.a.bcf /tmp/KeutieM3kJ/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/KeutieM3kJ/merge.2.a.vcf.gz /tmp/KeutieM3kJ/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/KeutieM3kJ/merge.2.a.vcf.gz /tmp/KeutieM3kJ/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/KeutieM3kJ/merge.2.a.bcf /tmp/KeutieM3kJ/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/KeutieM3kJ/merge.2.a.bcf /tmp/KeutieM3kJ/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/KeutieM3kJ/merge.3.a.vcf.gz /tmp/KeutieM3kJ/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/KeutieM3kJ/merge.3.a.vcf.gz /tmp/KeutieM3kJ/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/KeutieM3kJ/merge.3.a.bcf /tmp/KeutieM3kJ/merge.3.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/KeutieM3kJ/merge.3.a.bcf /tmp/KeutieM3kJ/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/KeutieM3kJ/merge.4.a.vcf.gz /tmp/KeutieM3kJ/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/KeutieM3kJ/merge.4.a.vcf.gz /tmp/KeutieM3kJ/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/KeutieM3kJ/merge.4.a.bcf /tmp/KeutieM3kJ/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/KeutieM3kJ/merge.4.a.bcf /tmp/KeutieM3kJ/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/gvcf.merge.1.vcf.gz /tmp/KeutieM3kJ/gvcf.merge.2.vcf.gz /tmp/KeutieM3kJ/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/gvcf.merge.1.vcf.gz /tmp/KeutieM3kJ/gvcf.merge.2.vcf.gz /tmp/KeutieM3kJ/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/gvcf.merge.1.bcf /tmp/KeutieM3kJ/gvcf.merge.2.bcf /tmp/KeutieM3kJ/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/gvcf.merge.1.bcf /tmp/KeutieM3kJ/gvcf.merge.2.bcf /tmp/KeutieM3kJ/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.2.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.2.b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.2.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.2.b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - -i SRC:join /tmp/KeutieM3kJ/merge.gvcf.3.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - -i SRC:join /tmp/KeutieM3kJ/merge.gvcf.3.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.4.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.4.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.4.a.bcf /tmp/KeutieM3kJ/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.4.a.bcf /tmp/KeutieM3kJ/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.5.a.vcf.gz /tmp/KeutieM3kJ/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.5.a.vcf.gz /tmp/KeutieM3kJ/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.5.a.bcf /tmp/KeutieM3kJ/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.5.a.bcf /tmp/KeutieM3kJ/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.6.a.vcf.gz /tmp/KeutieM3kJ/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.6.a.vcf.gz /tmp/KeutieM3kJ/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.6.a.bcf /tmp/KeutieM3kJ/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.6.a.bcf /tmp/KeutieM3kJ/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.7.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.7.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.7.a.bcf /tmp/KeutieM3kJ/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.7.a.bcf /tmp/KeutieM3kJ/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.8.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.8.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/KeutieM3kJ/merge.gvcf.8.a.bcf /tmp/KeutieM3kJ/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/KeutieM3kJ/merge.gvcf.8.a.bcf /tmp/KeutieM3kJ/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/KeutieM3kJ/merge.7.a.vcf.gz /tmp/KeutieM3kJ/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/KeutieM3kJ/merge.7.a.vcf.gz /tmp/KeutieM3kJ/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/KeutieM3kJ/merge.7.a.bcf /tmp/KeutieM3kJ/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/KeutieM3kJ/merge.7.a.bcf /tmp/KeutieM3kJ/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf /tmp/KeutieM3kJ/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf /tmp/KeutieM3kJ/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9c.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9d.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf /tmp/KeutieM3kJ/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/KeutieM3kJ/merge.gvcf.9a.bcf /tmp/KeutieM3kJ/merge.gvcf.9b.bcf /tmp/KeutieM3kJ/merge.gvcf.9c.bcf /tmp/KeutieM3kJ/merge.gvcf.9d.bcf /tmp/KeutieM3kJ/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.b.vcf.gz /tmp/KeutieM3kJ/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/KeutieM3kJ/merge.gvcf.10.b.bcf /tmp/KeutieM3kJ/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.noidx.a.vcf.gz /tmp/KeutieM3kJ/merge.noidx.b.vcf.gz /tmp/KeutieM3kJ/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.noidx.a.vcf.gz /tmp/KeutieM3kJ/merge.noidx.b.vcf.gz /tmp/KeutieM3kJ/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.noidx.a.bcf /tmp/KeutieM3kJ/merge.noidx.b.bcf /tmp/KeutieM3kJ/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.noidx.a.bcf /tmp/KeutieM3kJ/merge.noidx.b.bcf /tmp/KeutieM3kJ/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.c.vcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version --no-index /tmp/KeutieM3kJ/merge.noidx.a.bcf /tmp/KeutieM3kJ/merge.noidx.b.bcf /tmp/KeutieM3kJ/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob --no-index /tmp/KeutieM3kJ/merge.noidx.a.bcf /tmp/KeutieM3kJ/merge.noidx.b.bcf /tmp/KeutieM3kJ/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.8.a.vcf.gz /tmp/KeutieM3kJ/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.8.a.vcf.gz /tmp/KeutieM3kJ/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.8.a.bcf /tmp/KeutieM3kJ/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.8.a.bcf /tmp/KeutieM3kJ/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.8.a.vcf.gz /tmp/KeutieM3kJ/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.8.a.vcf.gz /tmp/KeutieM3kJ/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.8.a.bcf /tmp/KeutieM3kJ/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.8.a.bcf /tmp/KeutieM3kJ/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.9.a.vcf.gz /tmp/KeutieM3kJ/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.9.a.vcf.gz /tmp/KeutieM3kJ/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version /tmp/KeutieM3kJ/merge.9.a.bcf /tmp/KeutieM3kJ/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob /tmp/KeutieM3kJ/merge.9.a.bcf /tmp/KeutieM3kJ/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.9.a.vcf.gz /tmp/KeutieM3kJ/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.9.a.vcf.gz /tmp/KeutieM3kJ/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.9.a.bcf /tmp/KeutieM3kJ/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/KeutieM3kJ/merge.9.a.bcf /tmp/KeutieM3kJ/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/KeutieM3kJ/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/KeutieM3kJ/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/KeutieM3kJ/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' /tmp/KeutieM3kJ/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/KeutieM3kJ/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/KeutieM3kJ/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/KeutieM3kJ/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/KeutieM3kJ/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/KeutieM3kJ/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/KeutieM3kJ/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/KeutieM3kJ/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/KeutieM3kJ/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/KeutieM3kJ/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/KeutieM3kJ/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%LINE' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/KeutieM3kJ/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/KeutieM3kJ/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/KeutieM3kJ/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/KeutieM3kJ/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/KeutieM3kJ/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/KeutieM3kJ/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/KeutieM3kJ/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/KeutieM3kJ/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/KeutieM3kJ/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/KeutieM3kJ/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/KeutieM3kJ/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/KeutieM3kJ/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/KeutieM3kJ/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/KeutieM3kJ/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/KeutieM3kJ/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/KeutieM3kJ/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.56.out' /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.56.out' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/KeutieM3kJ/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/KeutieM3kJ/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/KeutieM3kJ/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/KeutieM3kJ/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/KeutieM3kJ/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/KeutieM3kJ/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/KeutieM3kJ/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/KeutieM3kJ/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/KeutieM3kJ/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/KeutieM3kJ/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/KeutieM3kJ/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/KeutieM3kJ/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/KeutieM3kJ/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/KeutieM3kJ/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/KeutieM3kJ/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/KeutieM3kJ/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/KeutieM3kJ/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/KeutieM3kJ/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/KeutieM3kJ/query.filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/KeutieM3kJ/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/KeutieM3kJ/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/KeutieM3kJ/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/KeutieM3kJ/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/KeutieM3kJ/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/KeutieM3kJ/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/KeutieM3kJ/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/KeutieM3kJ/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt /tmp/KeutieM3kJ/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt /tmp/KeutieM3kJ/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt /tmp/KeutieM3kJ/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/KeutieM3kJ/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/KeutieM3kJ/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/KeutieM3kJ/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/KeutieM3kJ/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/KeutieM3kJ/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/KeutieM3kJ/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- --force /tmp/KeutieM3kJ/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- --force /tmp/KeutieM3kJ/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/KeutieM3kJ/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/KeutieM3kJ/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- --keep-sum AD /tmp/KeutieM3kJ/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- --keep-sum AD /tmp/KeutieM3kJ/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/KeutieM3kJ/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/KeutieM3kJ/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/KeutieM3kJ/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/KeutieM3kJ/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/KeutieM3kJ/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/KeutieM3kJ/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m+ -s /tmp/KeutieM3kJ/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m+ -s /tmp/KeutieM3kJ/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.setref.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.telomere.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa /tmp/KeutieM3kJ/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/KeutieM3kJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/KeutieM3kJ/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/KeutieM3kJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/KeutieM3kJ/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/KeutieM3kJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/KeutieM3kJ/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d all /tmp/KeutieM3kJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d all /tmp/KeutieM3kJ/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/KeutieM3kJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/KeutieM3kJ/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/KeutieM3kJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/KeutieM3kJ/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d any /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d any /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/KeutieM3kJ/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -a -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.2.fa /tmp/KeutieM3kJ/norm.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -a -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.2.fa /tmp/KeutieM3kJ/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.iupac.fa /tmp/KeutieM3kJ/norm.iupac.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.iupac.fa /tmp/KeutieM3kJ/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.3.fa /tmp/KeutieM3kJ/norm.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.3.fa /tmp/KeutieM3kJ/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/KeutieM3kJ/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . /tmp/KeutieM3kJ/atomize.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . /tmp/KeutieM3kJ/atomize.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m +both /tmp/KeutieM3kJ/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m +both /tmp/KeutieM3kJ/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm --no-version -m +any /tmp/KeutieM3kJ/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools norm -Ob -m +any /tmp/KeutieM3kJ/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -f PASS -Xks NA00003 /tmp/KeutieM3kJ/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -f PASS -Xks NA00003 /tmp/KeutieM3kJ/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -xs NA00003 /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -xs NA00003 /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -p /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -p /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -P /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -P /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Hu /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -GVsnps /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -GVsnps /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -s ^NA00003 /tmp/KeutieM3kJ/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -s ^NA00003 /tmp/KeutieM3kJ/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version /tmp/KeutieM3kJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -G /tmp/KeutieM3kJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -G /tmp/KeutieM3kJ/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -HG /tmp/KeutieM3kJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -a /tmp/KeutieM3kJ/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -a /tmp/KeutieM3kJ/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asA /tmp/KeutieM3kJ/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asA /tmp/KeutieM3kJ/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asB /tmp/KeutieM3kJ/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asB /tmp/KeutieM3kJ/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -asA /tmp/KeutieM3kJ/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -asA /tmp/KeutieM3kJ/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i'TXT0="text"' /tmp/KeutieM3kJ/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.chrs.tab /tmp/KeutieM3kJ/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.chrs.tab /tmp/KeutieM3kJ/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -i 'POS>=3062917' /tmp/KeutieM3kJ/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -i 'POS>=3062917' /tmp/KeutieM3kJ/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/KeutieM3kJ/idx.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/KeutieM3kJ/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.2.bed /tmp/KeutieM3kJ/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.3.bed /tmp/KeutieM3kJ/idx.3.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/idx.4.bed /tmp/KeutieM3kJ/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Ht 2 /tmp/KeutieM3kJ/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -Ht 3 /tmp/KeutieM3kJ/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/KeutieM3kJ/overlap.vcf.gz .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -C5:nonmajor /tmp/KeutieM3kJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -c6:nonmajor /tmp/KeutieM3kJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -q0.3:major /tmp/KeutieM3kJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/KeutieM3kJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/KeutieM3kJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/KeutieM3kJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -H -a /tmp/KeutieM3kJ/view-a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt /tmp/KeutieM3kJ/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt /tmp/KeutieM3kJ/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt.gz /tmp/KeutieM3kJ/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.sites.txt.gz /tmp/KeutieM3kJ/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/KeutieM3kJ/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/regions.tab /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KeutieM3kJ/regions.tab.gz /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KeutieM3kJ/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/KeutieM3kJ/regions.tab.gz /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KeutieM3kJ/regions.bed /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KeutieM3kJ/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/KeutieM3kJ/regions.bed /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KeutieM3kJ/regions.bed.gz /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/KeutieM3kJ/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/KeutieM3kJ/regions.bed.gz /tmp/KeutieM3kJ/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/KeutieM3kJ/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/KeutieM3kJ/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots4.vcf.gz -c +INFO /tmp/KeutieM3kJ/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots4.vcf.gz -c +INFO /tmp/KeutieM3kJ/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots11.vcf.gz -c FMT /tmp/KeutieM3kJ/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots11.vcf.gz -c FMT /tmp/KeutieM3kJ/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots2.vcf.gz -c FMT/newGT:=GT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots2.vcf.gz -c FMT/newGT:=GT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots12.vcf.gz -c FMT/GT:=newGT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots12.vcf.gz -c FMT/GT:=newGT /tmp/KeutieM3kJ/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/KeutieM3kJ/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/KeutieM3kJ/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/KeutieM3kJ/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/KeutieM3kJ/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate20.src.vcf.gz -c FMT/GT /tmp/KeutieM3kJ/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate20.src.vcf.gz -c FMT/GT /tmp/KeutieM3kJ/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate20.src.vcf.gz -c +FMT/GT /tmp/KeutieM3kJ/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate20.src.vcf.gz -c +FMT/GT /tmp/KeutieM3kJ/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate20.src.vcf.gz -c -FMT/GT /tmp/KeutieM3kJ/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate20.src.vcf.gz -c -FMT/GT /tmp/KeutieM3kJ/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/KeutieM3kJ/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/KeutieM3kJ/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate24.src.vcf.gz -c XX /tmp/KeutieM3kJ/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate24.src.vcf.gz -c XX /tmp/KeutieM3kJ/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots.id.vcf.gz -c ALT /tmp/KeutieM3kJ/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots.id.vcf.gz -c ALT /tmp/KeutieM3kJ/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -a /tmp/KeutieM3kJ/annots.id.vcf.gz -c +ALT /tmp/KeutieM3kJ/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/KeutieM3kJ/annots.id.vcf.gz -c +ALT /tmp/KeutieM3kJ/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/KeutieM3kJ/checkploidy.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/KeutieM3kJ/checkploidy.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/KeutieM3kJ/checkploidy.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/KeutieM3kJ/checkploidy.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/KeutieM3kJ/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/KeutieM3kJ/checkploidy.2.bcf -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/KeutieM3kJ/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/KeutieM3kJ/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +setGT --no-version /tmp/KeutieM3kJ/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/KeutieM3kJ/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/KeutieM3kJ/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/KeutieM3kJ/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/KeutieM3kJ/dosage.bcf -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/KeutieM3kJ/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/KeutieM3kJ/dosage.bcf -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/KeutieM3kJ/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +dosage /tmp/KeutieM3kJ/dosage.bcf -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/KeutieM3kJ/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/KeutieM3kJ/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/KeutieM3kJ/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/KeutieM3kJ/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/KeutieM3kJ/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +guess-ploidy /tmp/KeutieM3kJ/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/KeutieM3kJ/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/KeutieM3kJ/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/KeutieM3kJ/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/KeutieM3kJ/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +add-variantkey /tmp/KeutieM3kJ/query.variantkey.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +add-variantkey /tmp/KeutieM3kJ/query.variantkey.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +variantkey-hex /tmp/KeutieM3kJ/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +variantkey-hex /tmp/KeutieM3kJ/query.variantkey.bcf test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +allele-length /tmp/KeutieM3kJ/query.nucleotide.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +allele-length /tmp/KeutieM3kJ/query.nucleotide.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hemi.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hwe.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.vcf.gz -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.vcf.gz -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/KeutieM3kJ/fill-tags-AD.bcf -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTisec /tmp/KeutieM3kJ/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/KeutieM3kJ/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/KeutieM3kJ/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/KeutieM3kJ/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/KeutieM3kJ/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/KeutieM3kJ/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-stats /tmp/KeutieM3kJ/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +smpl-stats /tmp/KeutieM3kJ/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +smpl-stats /tmp/KeutieM3kJ/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/KeutieM3kJ/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/KeutieM3kJ/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/KeutieM3kJ/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/KeutieM3kJ/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/KeutieM3kJ/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +indel-stats /tmp/KeutieM3kJ/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +ad-bias /tmp/KeutieM3kJ/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +af-dist /tmp/KeutieM3kJ/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +af-dist /tmp/KeutieM3kJ/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/KeutieM3kJ/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -i /tmp/KeutieM3kJ/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fixref /tmp/KeutieM3kJ/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/KeutieM3kJ/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/KeutieM3kJ/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/KeutieM3kJ/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/KeutieM3kJ/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/KeutieM3kJ/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/KeutieM3kJ/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/KeutieM3kJ/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/KeutieM3kJ/view.bcf -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/KeutieM3kJ/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/KeutieM3kJ/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/KeutieM3kJ/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/KeutieM3kJ/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +mendelian /tmp/KeutieM3kJ/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +contrast /tmp/KeutieM3kJ/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/KeutieM3kJ/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/KeutieM3kJ/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/KeutieM3kJ/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/KeutieM3kJ/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/KeutieM3kJ/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/KeutieM3kJ/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +gvcfz /tmp/KeutieM3kJ/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/KeutieM3kJ/remove-overlaps.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/KeutieM3kJ/remove-overlaps.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/KeutieM3kJ/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +remove-overlaps /tmp/KeutieM3kJ/remove-overlaps.bcf -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.3.vcf.gz -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.3.bcf -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.8.vcf.gz -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.8.bcf -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.9.vcf.gz -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.9.bcf -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.10.vcf.gz -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.10.bcf -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.10.vcf.gz -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split-vep /tmp/KeutieM3kJ/split-vep.10.bcf -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +parental-origin /tmp/KeutieM3kJ/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/KeutieM3kJ/prune.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/KeutieM3kJ/prune.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/KeutieM3kJ/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/KeutieM3kJ/prune.1.bcf | grep -v ^##bcftools_ .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.1 && cd /tmp/KeutieM3kJ/split.1.1 && for f in A1.vcf A2.vcf A3.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.2 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.2.txt && cd /tmp/KeutieM3kJ/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.3 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt && cd /tmp/KeutieM3kJ/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.4 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/KeutieM3kJ/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.5 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/KeutieM3kJ/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.6 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/KeutieM3kJ/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.1.vcf -o /tmp/KeutieM3kJ/split.1.7 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.grp.1.1.txt && cd /tmp/KeutieM3kJ/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/split.2.vcf -o /tmp/KeutieM3kJ/split.2.1 && cd /tmp/KeutieM3kJ/split.2.1 && for f in A1_A1-1.vcf A1_A1-2.vcf A1_A1.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/KeutieM3kJ/scatter.1.1 -n 3 && cd /tmp/KeutieM3kJ/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/KeutieM3kJ/scatter.1.2 -s 21,22 && cd /tmp/KeutieM3kJ/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/KeutieM3kJ/scatter.1.3 -s 21,22 -x X && cd /tmp/KeutieM3kJ/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^## .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version /tmp/KeutieM3kJ/concat.1.a.vcf.gz /tmp/KeutieM3kJ/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/KeutieM3kJ/concat.1.a.vcf.gz /tmp/KeutieM3kJ/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version /tmp/KeutieM3kJ/concat.1.a.bcf /tmp/KeutieM3kJ/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob /tmp/KeutieM3kJ/concat.1.a.bcf /tmp/KeutieM3kJ/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -a /tmp/KeutieM3kJ/concat.2.a.vcf.gz /tmp/KeutieM3kJ/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -a /tmp/KeutieM3kJ/concat.2.a.vcf.gz /tmp/KeutieM3kJ/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -a /tmp/KeutieM3kJ/concat.2.a.bcf /tmp/KeutieM3kJ/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -a /tmp/KeutieM3kJ/concat.2.a.bcf /tmp/KeutieM3kJ/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/KeutieM3kJ/concat.2.a.vcf.gz /tmp/KeutieM3kJ/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/KeutieM3kJ/concat.2.a.vcf.gz /tmp/KeutieM3kJ/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/KeutieM3kJ/concat.2.a.bcf /tmp/KeutieM3kJ/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/KeutieM3kJ/concat.2.a.bcf /tmp/KeutieM3kJ/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/KeutieM3kJ/concat.3.a.vcf.gz /tmp/KeutieM3kJ/concat.3.b.vcf.gz /tmp/KeutieM3kJ/concat.3.0.vcf.gz /tmp/KeutieM3kJ/concat.3.c.vcf.gz /tmp/KeutieM3kJ/concat.3.d.vcf.gz /tmp/KeutieM3kJ/concat.3.e.vcf.gz /tmp/KeutieM3kJ/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/KeutieM3kJ/concat.3.a.vcf.gz /tmp/KeutieM3kJ/concat.3.b.vcf.gz /tmp/KeutieM3kJ/concat.3.0.vcf.gz /tmp/KeutieM3kJ/concat.3.c.vcf.gz /tmp/KeutieM3kJ/concat.3.d.vcf.gz /tmp/KeutieM3kJ/concat.3.e.vcf.gz /tmp/KeutieM3kJ/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/KeutieM3kJ/concat.3.a.bcf /tmp/KeutieM3kJ/concat.3.b.bcf /tmp/KeutieM3kJ/concat.3.0.bcf /tmp/KeutieM3kJ/concat.3.c.bcf /tmp/KeutieM3kJ/concat.3.d.bcf /tmp/KeutieM3kJ/concat.3.e.bcf /tmp/KeutieM3kJ/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/KeutieM3kJ/concat.3.a.bcf /tmp/KeutieM3kJ/concat.3.b.bcf /tmp/KeutieM3kJ/concat.3.0.bcf /tmp/KeutieM3kJ/concat.3.c.bcf /tmp/KeutieM3kJ/concat.3.d.bcf /tmp/KeutieM3kJ/concat.3.e.bcf /tmp/KeutieM3kJ/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2850346156 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive-force /tmp/KeutieM3kJ/naive_concat.0.bcf /tmp/KeutieM3kJ/naive_concat.1.bcf /tmp/KeutieM3kJ/naive_concat.2.bcf /tmp/KeutieM3kJ/naive_concat.3.bcf /tmp/KeutieM3kJ/naive_concat.4.bcf /tmp/KeutieM3kJ/naive_concat.5.bcf /tmp/KeutieM3kJ/naive_concat.6.bcf /tmp/KeutieM3kJ/naive_concat.7.bcf /tmp/KeutieM3kJ/naive_concat.8.bcf /tmp/KeutieM3kJ/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --naive /tmp/KeutieM3kJ/naive_concat.0.vcf.gz /tmp/KeutieM3kJ/naive_concat.1.vcf.gz /tmp/KeutieM3kJ/naive_concat.2.vcf.gz /tmp/KeutieM3kJ/naive_concat.3.vcf.gz /tmp/KeutieM3kJ/naive_concat.4.vcf.gz /tmp/KeutieM3kJ/naive_concat.5.vcf.gz /tmp/KeutieM3kJ/naive_concat.6.vcf.gz /tmp/KeutieM3kJ/naive_concat.7.vcf.gz /tmp/KeutieM3kJ/naive_concat.8.vcf.gz /tmp/KeutieM3kJ/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -H .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l /tmp/KeutieM3kJ/concat.4.a.vcf.gz /tmp/KeutieM3kJ/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l /tmp/KeutieM3kJ/concat.4.a.vcf.gz /tmp/KeutieM3kJ/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l /tmp/KeutieM3kJ/concat.4.a.bcf /tmp/KeutieM3kJ/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l /tmp/KeutieM3kJ/concat.4.a.bcf /tmp/KeutieM3kJ/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/KeutieM3kJ/concat.5.a.vcf.gz /tmp/KeutieM3kJ/concat.5.b.vcf.gz /tmp/KeutieM3kJ/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/KeutieM3kJ/concat.5.a.vcf.gz /tmp/KeutieM3kJ/concat.5.b.vcf.gz /tmp/KeutieM3kJ/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/KeutieM3kJ/concat.5.a.bcf /tmp/KeutieM3kJ/concat.5.b.bcf /tmp/KeutieM3kJ/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/KeutieM3kJ/concat.5.a.bcf /tmp/KeutieM3kJ/concat.5.b.bcf /tmp/KeutieM3kJ/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat --no-version -l --ligate-force /tmp/KeutieM3kJ/concat.5.a.bcf /tmp/KeutieM3kJ/concat.5.b.bcf /tmp/KeutieM3kJ/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools concat -Ob -l --ligate-force /tmp/KeutieM3kJ/concat.5.a.bcf /tmp/KeutieM3kJ/concat.5.b.bcf /tmp/KeutieM3kJ/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /tmp/KeutieM3kJ/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr /tmp/KeutieM3kJ/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/KeutieM3kJ/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/KeutieM3kJ/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/KeutieM3kJ/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/KeutieM3kJ/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/reheader.fai /tmp/KeutieM3kJ/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/KeutieM3kJ/rename.map -Ov /tmp/KeutieM3kJ/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/KeutieM3kJ/rename.map -Ob /tmp/KeutieM3kJ/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/KeutieM3kJ/rename.map -Ov /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/KeutieM3kJ/rename.map -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --3N6 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.3N6.gen,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --tag PL /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/KeutieM3kJ/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids /tmp/KeutieM3kJ/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 /tmp/KeutieM3kJ/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 /tmp/KeutieM3kJ/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids /tmp/KeutieM3kJ/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids /tmp/KeutieM3kJ/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h -,.,. /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,.,- /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. /tmp/KeutieM3kJ/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample .,- /tmp/KeutieM3kJ/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa /tmp/KeutieM3kJ/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view -Ob /tmp/KeutieM3kJ/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/convert.23andme | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/KeutieM3kJ/consensus.1.chain.new >/dev/null; cat /tmp/KeutieM3kJ/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/KeutieM3kJ/consensus.2.chain.new >/dev/null; cat /tmp/KeutieM3kJ/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.tab -c /tmp/KeutieM3kJ/consensus.3.chain.new >/dev/null; cat /tmp/KeutieM3kJ/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H 1 -c /tmp/KeutieM3kJ/consensus.4.chain.new >/dev/null; cat /tmp/KeutieM3kJ/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus6.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.12.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.13.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.14.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.fa -H I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus2.fa -M N -m /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.17.bed .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.18.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools consensus /tmp/KeutieM3kJ/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/consensus.19.fa .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/KeutieM3kJ/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/KeutieM3kJ/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/KeutieM3kJ/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/KeutieM3kJ/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.gff3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p s1,s1 /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/KeutieM3kJ/gtcheck.2.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.3.pairs /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 --n-matches 4 /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,C,B,D /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT -H /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL -H /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT -H /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL -H /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/KeutieM3kJ/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/KeutieM3kJ/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u GT -e 300 /tmp/KeutieM3kJ/gtcheck.1.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck -u PL -e 30 /tmp/KeutieM3kJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck /tmp/KeutieM3kJ/gtcheck.ntop.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck --n-matches 2 /tmp/KeutieM3kJ/gtcheck.ntop.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/bcftools gtcheck /tmp/KeutieM3kJ/gtcheck.5.vcf.gz -g /tmp/KeutieM3kJ/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1725 passed .. 1725 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.15.1-13.fc43.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hqpkna + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd bcftools-1.15.1 + DOCDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/AUTHORS /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/NEWS /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.i3V8VQ + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + cd bcftools-1.15.1 + LICENSEDIR=/builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + cp -pr /builddir/build/BUILD/bcftools-1.15.1-build/bcftools-1.15.1/LICENSE /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.15.1-13.fc43 bcftools(x86-64) = 1.15.1-13.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgsl.so.28()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.41()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.15.1-13.fc43.x86_64 Provides: bcftools-debugsource = 1.15.1-13.fc43 bcftools-debugsource(x86-64) = 1.15.1-13.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.15.1-13.fc43.x86_64 Provides: bcftools-debuginfo = 1.15.1-13.fc43 bcftools-debuginfo(x86-64) = 1.15.1-13.fc43 debuginfo(build-id) = 0268eac535f4b59ed7e8d8728ea9024dc1facd9f debuginfo(build-id) = 04415b288d393f5be264ce946dfc9c242ed140f9 debuginfo(build-id) = 062dae17bcf3e2e1cff86feec1dec89e8815f7e0 debuginfo(build-id) = 0c55017b52f2dacfd3009c33d40af0d6b2f04bab debuginfo(build-id) = 1345b60770648a537c7e792b3e83f2e42c23ae00 debuginfo(build-id) = 2080340b15c417bffd5bb13a9acc10c36ae93d25 debuginfo(build-id) = 21221f9ec9f26c0b3136c06d47abc7a5f34ddc9a debuginfo(build-id) = 24175c80f8435eed513f0aca47f33df39f609696 debuginfo(build-id) = 2d275ec4abc87aceb991178c92e919aed20d2f09 debuginfo(build-id) = 31c012b0c5c800d9d0643c6225000248a28fede9 debuginfo(build-id) = 3500043394f5db5a7086f846177e15dbc2e8a610 debuginfo(build-id) = 3a76e84dca05c841a5cc335302b7db87a2e78b0e debuginfo(build-id) = 43a95df31c05e2cec9701af7f9fa0aa62ef28579 debuginfo(build-id) = 477f2ce8368a16045d30293ca2a4a2cc7e4149a5 debuginfo(build-id) = 522096caeee4d4239c8c90dc8362c1796214a74b debuginfo(build-id) = 5273a8009675e93a35d421c4885c348be30375c7 debuginfo(build-id) = 5756e155b12ec7c679cf77acc1d3af2f2ded2206 debuginfo(build-id) = 606d083cad4e0ac2cf3a800dc7607bfb653752f8 debuginfo(build-id) = 617d6f37891e2cc6d7f954678fef12392d349246 debuginfo(build-id) = 6390c75cb4d09d3e15112a1d6a4623abbb8bb14c debuginfo(build-id) = 6a41b947e6d779838d47b351ff05524fcc05eadd debuginfo(build-id) = 6ab0af45b01c7e83d0ae1bc81dfd806ac30bc546 debuginfo(build-id) = 6b540148438f64916bd2735f7b30d1f0e3aeda83 debuginfo(build-id) = 7f1220231535c3bc705b37d5cd30a7463c64ade0 debuginfo(build-id) = 8fd631e779bb41b6154d13cec72b8038dda0b085 debuginfo(build-id) = 9055ddebffd8b4ed97200b215b84bb9da36628d7 debuginfo(build-id) = 956ec4b0232aeb8f74c5d39591775029ba0f201b debuginfo(build-id) = 9e137a4788a40b60c31f2a07258c703ccf7c2eed debuginfo(build-id) = aba6ee95859804adf9abc7cbd119c6a77ebf9a5a debuginfo(build-id) = b0513a7a49fedb383509e0bc15b1955583f780fc debuginfo(build-id) = bdab32d98f02a7311160f62347b3021442087da1 debuginfo(build-id) = c88a4fd1b5e1f68f160ae0a6e88b8f283bade367 debuginfo(build-id) = d3cf6245b2af758c56e35544aff78cfcc7d51b68 debuginfo(build-id) = d7a01b7002195dd706f021eba1b8a2bbd645eda7 debuginfo(build-id) = d7ba49933f6d0b52a57c3e72248082e618665168 debuginfo(build-id) = edd36a8529879d7d1b2b1600fe8eeefab3255f97 debuginfo(build-id) = f0e95b82eb4c88dca18099f295b55b8b260debb6 debuginfo(build-id) = f62a87edd2610f6fc4aff4d7cb42060643e03fdc debuginfo(build-id) = ff5263225fa73faba4290755e6b7a64e1dd48c56 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-64) = 1.15.1-13.fc43 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bcftools-1.15.1-build/BUILDROOT Wrote: /builddir/build/RPMS/bcftools-1.15.1-13.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.15.1-13.fc43.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.15.1-13.fc43.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.hFpyEv + umask 022 + cd /builddir/build/BUILD/bcftools-1.15.1-build + test -d /builddir/build/BUILD/bcftools-1.15.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bcftools-1.15.1-build + rm -rf /builddir/build/BUILD/bcftools-1.15.1-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bcftools-1.15.1-13.fc43.src.rpm Finish: build phase for bcftools-1.15.1-13.fc43.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1746456050.955289/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/bcftools-1.15.1-13.fc43.src.rpm) Config(child) 1 minutes 4 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "bcftools", "epoch": null, "version": "1.15.1", "release": "13.fc43", "arch": "x86_64" }, { "name": "bcftools-debugsource", "epoch": null, "version": "1.15.1", "release": "13.fc43", "arch": "x86_64" }, { "name": "bcftools", "epoch": null, "version": "1.15.1", "release": "13.fc43", "arch": "src" }, { "name": "bcftools-debuginfo", "epoch": null, "version": "1.15.1", "release": "13.fc43", "arch": "x86_64" } ] } RPMResults finished