0s autopkgtest [19:38:30]: starting date and time: 2024-03-25 19:38:30+0000 0s autopkgtest [19:38:30]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [19:38:30]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pup3b628/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:bcftools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade bcftools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=bcftools/1.19-1build1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-11.secgroup --name adt-noble-ppc64el-bcftools-20240325-193830-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 93s autopkgtest [19:40:03]: testbed dpkg architecture: ppc64el 93s autopkgtest [19:40:03]: testbed apt version: 2.7.12 93s autopkgtest [19:40:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 95s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 95s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3992 kB] 97s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 97s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 97s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 97s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 97s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4231 kB] 98s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 98s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 98s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 101s Fetched 9677 kB in 5s (2004 kB/s) 102s Reading package lists... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s The following packages will be REMOVED: 105s libssl3 105s The following NEW packages will be installed: 105s libssl3t64 105s The following packages have been kept back: 105s curl 105s The following packages will be upgraded: 105s openssl 105s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 105s Need to get 3151 kB of archives. 105s After this operation, 73.7 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 106s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 107s Fetched 3151 kB in 1s (2502 kB/s) 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70156 files and directories currently installed.) 107s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 107s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 107s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 107s wget depends on libssl3 (>= 3.0.0). 107s tnftp depends on libssl3 (>= 3.0.0). 107s tcpdump depends on libssl3 (>= 3.0.0). 107s systemd-resolved depends on libssl3 (>= 3.0.0). 107s systemd depends on libssl3 (>= 3.0.0). 107s sudo depends on libssl3 (>= 3.0.0). 107s rsync depends on libssl3 (>= 3.0.0). 107s python3-cryptography depends on libssl3 (>= 3.0.0). 107s openssh-server depends on libssl3 (>= 3.0.10). 107s openssh-client depends on libssl3 (>= 3.0.10). 107s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 107s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 107s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 107s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 107s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 107s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 107s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 107s libnvme1 depends on libssl3 (>= 3.0.0). 107s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 107s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 107s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 107s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 107s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 107s kmod depends on libssl3 (>= 3.0.0). 107s dhcpcd-base depends on libssl3 (>= 3.0.0). 107s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 107s 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70156 files and directories currently installed.) 107s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 107s Selecting previously unselected package libssl3t64:ppc64el. 107s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70145 files and directories currently installed.) 107s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 107s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 107s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 107s Setting up openssl (3.0.13-0ubuntu2) ... 107s Processing triggers for man-db (2.12.0-3) ... 108s Processing triggers for libc-bin (2.39-0ubuntu6) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 109s sh: Attempting to set up Debian/Ubuntu apt sources automatically 109s sh: Distribution appears to be Ubuntu 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s eatmydata is already the newest version (131-1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s dbus is already the newest version (1.14.10-4ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s rng-tools-debian is already the newest version (2.4). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s The following packages will be REMOVED: 111s cloud-init* python3-configobj* python3-debconf* 112s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 112s After this operation, 3256 kB disk space will be freed. 112s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70158 files and directories currently installed.) 112s Removing cloud-init (24.1.2-0ubuntu1) ... 112s Removing python3-configobj (5.0.8-3) ... 112s Removing python3-debconf (1.5.86) ... 112s Processing triggers for man-db (2.12.0-3) ... 113s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69769 files and directories currently installed.) 113s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 113s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 113s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 113s invoke-rc.d: policy-rc.d denied execution of try-restart. 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s linux-generic is already the newest version (6.8.0-11.11+1). 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 114s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 117s Reading package lists... 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [19:40:28]: rebooting testbed after setup commands that affected boot 283s autopkgtest [19:43:12]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 286s autopkgtest [19:43:16]: @@@@@@@@@@@@@@@@@@@@ apt-source bcftools 290s Get:1 http://ftpmaster.internal/ubuntu noble/universe bcftools 1.19-1 (dsc) [2270 B] 290s Get:2 http://ftpmaster.internal/ubuntu noble/universe bcftools 1.19-1 (tar) [3540 kB] 290s Get:3 http://ftpmaster.internal/ubuntu noble/universe bcftools 1.19-1 (diff) [11.1 kB] 290s gpgv: Signature made Fri Dec 15 11:45:44 2023 UTC 290s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 290s gpgv: issuer "emollier@debian.org" 290s gpgv: Can't check signature: No public key 290s dpkg-source: warning: cannot verify inline signature for ./bcftools_1.19-1.dsc: no acceptable signature found 290s autopkgtest [19:43:20]: testing package bcftools version 1.19-1 291s autopkgtest [19:43:21]: build not needed 295s autopkgtest [19:43:25]: test command1: preparing testbed 299s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s Starting pkgProblemResolver with broken count: 0 299s Starting 2 pkgProblemResolver with broken count: 0 299s Done 300s The following additional packages will be installed: 300s bcftools libdeflate0 libhts3 libhtscodecs2 tabix 300s Suggested packages: 300s python3-numpy python3-matplotlib texlive-latex-recommended 300s The following NEW packages will be installed: 300s autopkgtest-satdep bcftools libdeflate0 libhts3 libhtscodecs2 tabix 300s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 300s Need to get 2392 kB/2393 kB of archives. 300s After this operation, 10.4 MB of additional disk space will be used. 300s Get:1 /tmp/autopkgtest.ig2rlO/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 300s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 300s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 300s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 300s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el bcftools ppc64el 1.19-1 [976 kB] 301s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el tabix ppc64el 1.18+ds-1 [692 kB] 301s Fetched 2392 kB in 2s (1543 kB/s) 301s Selecting previously unselected package libdeflate0:ppc64el. 301s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69714 files and directories currently installed.) 301s Preparing to unpack .../0-libdeflate0_1.19-1_ppc64el.deb ... 301s Unpacking libdeflate0:ppc64el (1.19-1) ... 301s Selecting previously unselected package libhtscodecs2:ppc64el. 301s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_ppc64el.deb ... 301s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 301s Selecting previously unselected package libhts3:ppc64el. 301s Preparing to unpack .../2-libhts3_1.18+ds-1_ppc64el.deb ... 301s Unpacking libhts3:ppc64el (1.18+ds-1) ... 302s Selecting previously unselected package bcftools. 302s Preparing to unpack .../3-bcftools_1.19-1_ppc64el.deb ... 302s Unpacking bcftools (1.19-1) ... 302s Selecting previously unselected package tabix. 302s Preparing to unpack .../4-tabix_1.18+ds-1_ppc64el.deb ... 302s Unpacking tabix (1.18+ds-1) ... 302s Selecting previously unselected package autopkgtest-satdep. 302s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 302s Unpacking autopkgtest-satdep (0) ... 302s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 302s Setting up libdeflate0:ppc64el (1.19-1) ... 302s Setting up tabix (1.18+ds-1) ... 302s Setting up libhts3:ppc64el (1.18+ds-1) ... 302s Setting up bcftools (1.19-1) ... 302s Setting up autopkgtest-satdep (0) ... 302s Processing triggers for man-db (2.12.0-3) ... 302s Processing triggers for libc-bin (2.39-0ubuntu6) ... 305s (Reading database ... 69803 files and directories currently installed.) 305s Removing autopkgtest-satdep (0) ... 306s autopkgtest [19:43:36]: test command1: mv -f bcftools bcftools.orig || /bin/true; ln -s /usr/bin/bcftools bcftools && ./test/test.pl --exec bgzip=/usr/bin/bgzip --exec tabix=/usr/bin/tabix && mv -f bcftools.orig bcftools || /bin/true 306s autopkgtest [19:43:36]: test command1: [----------------------- 306s mv: cannot stat 'bcftools': No such file or directory 306s ./test/test.pl: module IO::Pty not found; skipping usage tests 306s test_usage: 306s bcftools 306s test_tabix: 306s /usr/bin/tabix /tmp/Luz3rC8Wiv/merge.a.vcf.gz 2:3199812-3199812 306s .. ok 306s 306s test_tabix: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/merge.a.bcf 2:3199812-3199812 306s .. ok 306s 306s test_tabix: 306s /usr/bin/tabix /tmp/Luz3rC8Wiv/merge.a.vcf.gz 1:3000151-3000151 306s .. ok 306s 306s test_tabix: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/merge.a.bcf 1:3000151-3000151 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.bcf chr20:1-2147483647 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.bcf chr20:1-2147483647 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.bcf chr20:1-2147483647 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.vcf.gz chr20 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.bcf chr20 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.bcf chr20 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.vcf.gz chr20 306s .. ok 306s 306s test_index: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H /tmp/Luz3rC8Wiv/large_chrom_csi_limit.bcf chr20 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -s /tmp/Luz3rC8Wiv/idx.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -s /tmp/Luz3rC8Wiv/idx.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -s /tmp/Luz3rC8Wiv/idx.bcf 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/idx.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/idx.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/idx.vcf.gz.csi 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/idx.bcf 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/idx.bcf.csi 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -s /tmp/Luz3rC8Wiv/empty.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -s /tmp/Luz3rC8Wiv/empty.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -s /tmp/Luz3rC8Wiv/empty.bcf 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/empty.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/empty.vcf.gz 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/empty.vcf.gz.csi 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/empty.bcf 306s .. ok 306s 306s test_vcf_idxstats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools index -n /tmp/Luz3rC8Wiv/empty.bcf.csi 306s .. ok 306s 306s test_vcf_check: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s - /tmp/Luz3rC8Wiv/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_check: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_check_merge: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/misc/plot-vcfstats -m /tmp/Luz3rC8Wiv/check.1.chk /tmp/Luz3rC8Wiv/check.2.chk /tmp/Luz3rC8Wiv/check.3.chk /tmp/Luz3rC8Wiv/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_stats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s - /tmp/Luz3rC8Wiv/stats.a.vcf.gz /tmp/Luz3rC8Wiv/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_stats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s B /tmp/Luz3rC8Wiv/stats.a.vcf.gz /tmp/Luz3rC8Wiv/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_stats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s - /tmp/Luz3rC8Wiv/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_stats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s - -i 'type="snp"' /tmp/Luz3rC8Wiv/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_stats: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools stats -s - /tmp/Luz3rC8Wiv/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' 306s .. ok 306s 306s test_vcf_isec: 306s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -n =2 /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -n =2 /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -n =2 -c both /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -n =2 -c both /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -n =2 -c any /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -n =2 -c any /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -C -c any /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -C -c any /tmp/Luz3rC8Wiv/isec.a.vcf.gz /tmp/Luz3rC8Wiv/isec.b.vcf.gz 307s .. ok 307s 307s test_vcf_isec2: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec --no-version -T /tmp/Luz3rC8Wiv/isec.tab.gz /tmp/Luz3rC8Wiv/isec.a.vcf.gz 307s .. ok 307s 307s test_vcf_isec2: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -T /tmp/Luz3rC8Wiv/isec.tab.gz /tmp/Luz3rC8Wiv/isec.a.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Luz3rC8Wiv/isec-miss.1.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Luz3rC8Wiv/isec-miss.1.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/isec-miss.1.regs.txt -n +1 /tmp/Luz3rC8Wiv/isec-miss.1.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/isec-miss.1.regs.txt -n +1 /tmp/Luz3rC8Wiv/isec-miss.1.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.1.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Luz3rC8Wiv/isec-miss.2.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/Luz3rC8Wiv/isec-miss.2.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/isec-miss.1.regs.txt -n +1 /tmp/Luz3rC8Wiv/isec-miss.2.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.3.vcf.gz 307s .. ok 307s 307s test_vcf_isec: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools isec -Ob -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/isec-miss.1.regs.txt -n +1 /tmp/Luz3rC8Wiv/isec-miss.2.1.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.2.vcf.gz /tmp/Luz3rC8Wiv/isec-miss.2.3.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -i AF:join /tmp/Luz3rC8Wiv/merge.join.a.vcf.gz /tmp/Luz3rC8Wiv/merge.join.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -i AF:join /tmp/Luz3rC8Wiv/merge.join.a.vcf.gz /tmp/Luz3rC8Wiv/merge.join.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -i AF:join /tmp/Luz3rC8Wiv/merge.join.a.bcf /tmp/Luz3rC8Wiv/merge.join.b.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -i AF:join /tmp/Luz3rC8Wiv/merge.join.a.bcf /tmp/Luz3rC8Wiv/merge.join.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 1 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 1 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 2 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 2 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 3 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 3 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 4 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 4 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 5 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/Luz3rC8Wiv/merge.LPL.a.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.b.vcf.gz /tmp/Luz3rC8Wiv/merge.LPL.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -L 5 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/Luz3rC8Wiv/merge.LPL.a.bcf /tmp/Luz3rC8Wiv/merge.LPL.b.bcf /tmp/Luz3rC8Wiv/merge.LPL.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples /tmp/Luz3rC8Wiv/merge.a.vcf.gz /tmp/Luz3rC8Wiv/merge.b.vcf.gz /tmp/Luz3rC8Wiv/merge.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples /tmp/Luz3rC8Wiv/merge.a.vcf.gz /tmp/Luz3rC8Wiv/merge.b.vcf.gz /tmp/Luz3rC8Wiv/merge.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples /tmp/Luz3rC8Wiv/merge.a.bcf /tmp/Luz3rC8Wiv/merge.b.bcf /tmp/Luz3rC8Wiv/merge.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples /tmp/Luz3rC8Wiv/merge.a.bcf /tmp/Luz3rC8Wiv/merge.b.bcf /tmp/Luz3rC8Wiv/merge.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -Fx /tmp/Luz3rC8Wiv/merge.a.vcf.gz /tmp/Luz3rC8Wiv/merge.b.vcf.gz /tmp/Luz3rC8Wiv/merge.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -Fx /tmp/Luz3rC8Wiv/merge.a.vcf.gz /tmp/Luz3rC8Wiv/merge.b.vcf.gz /tmp/Luz3rC8Wiv/merge.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -Fx /tmp/Luz3rC8Wiv/merge.a.bcf /tmp/Luz3rC8Wiv/merge.b.bcf /tmp/Luz3rC8Wiv/merge.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -Fx /tmp/Luz3rC8Wiv/merge.a.bcf /tmp/Luz3rC8Wiv/merge.b.bcf /tmp/Luz3rC8Wiv/merge.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -0 /tmp/Luz3rC8Wiv/merge.a.vcf.gz /tmp/Luz3rC8Wiv/merge.b.vcf.gz /tmp/Luz3rC8Wiv/merge.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -0 /tmp/Luz3rC8Wiv/merge.a.vcf.gz /tmp/Luz3rC8Wiv/merge.b.vcf.gz /tmp/Luz3rC8Wiv/merge.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -0 /tmp/Luz3rC8Wiv/merge.a.bcf /tmp/Luz3rC8Wiv/merge.b.bcf /tmp/Luz3rC8Wiv/merge.c.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -0 /tmp/Luz3rC8Wiv/merge.a.bcf /tmp/Luz3rC8Wiv/merge.b.bcf /tmp/Luz3rC8Wiv/merge.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m none /tmp/Luz3rC8Wiv/merge.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.2.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m none /tmp/Luz3rC8Wiv/merge.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.2.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m none /tmp/Luz3rC8Wiv/merge.2.a.bcf /tmp/Luz3rC8Wiv/merge.2.b.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m none /tmp/Luz3rC8Wiv/merge.2.a.bcf /tmp/Luz3rC8Wiv/merge.2.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m both /tmp/Luz3rC8Wiv/merge.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.2.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m both /tmp/Luz3rC8Wiv/merge.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.2.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m both /tmp/Luz3rC8Wiv/merge.2.a.bcf /tmp/Luz3rC8Wiv/merge.2.b.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m both /tmp/Luz3rC8Wiv/merge.2.a.bcf /tmp/Luz3rC8Wiv/merge.2.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m all /tmp/Luz3rC8Wiv/merge.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.2.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m all /tmp/Luz3rC8Wiv/merge.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.2.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m all /tmp/Luz3rC8Wiv/merge.2.a.bcf /tmp/Luz3rC8Wiv/merge.2.b.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m all /tmp/Luz3rC8Wiv/merge.2.a.bcf /tmp/Luz3rC8Wiv/merge.2.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Luz3rC8Wiv/merge.3.a.vcf.gz /tmp/Luz3rC8Wiv/merge.3.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Luz3rC8Wiv/merge.3.a.vcf.gz /tmp/Luz3rC8Wiv/merge.3.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Luz3rC8Wiv/merge.3.a.bcf /tmp/Luz3rC8Wiv/merge.3.b.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/Luz3rC8Wiv/merge.3.a.bcf /tmp/Luz3rC8Wiv/merge.3.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m id /tmp/Luz3rC8Wiv/merge.4.a.vcf.gz /tmp/Luz3rC8Wiv/merge.4.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m id /tmp/Luz3rC8Wiv/merge.4.a.vcf.gz /tmp/Luz3rC8Wiv/merge.4.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples -m id /tmp/Luz3rC8Wiv/merge.4.a.bcf /tmp/Luz3rC8Wiv/merge.4.b.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples -m id /tmp/Luz3rC8Wiv/merge.4.a.bcf /tmp/Luz3rC8Wiv/merge.4.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/gvcf.merge.1.vcf.gz /tmp/Luz3rC8Wiv/gvcf.merge.2.vcf.gz /tmp/Luz3rC8Wiv/gvcf.merge.3.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/gvcf.merge.1.vcf.gz /tmp/Luz3rC8Wiv/gvcf.merge.2.vcf.gz /tmp/Luz3rC8Wiv/gvcf.merge.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/gvcf.merge.1.bcf /tmp/Luz3rC8Wiv/gvcf.merge.2.bcf /tmp/Luz3rC8Wiv/gvcf.merge.3.bcf 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/gvcf.merge.1.bcf /tmp/Luz3rC8Wiv/gvcf.merge.2.bcf /tmp/Luz3rC8Wiv/gvcf.merge.3.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - -m both,* /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - -m both,** /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.c.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - -i SRC:join /tmp/Luz3rC8Wiv/merge.gvcf.3.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.3.b.vcf.gz 307s .. ok 307s 307s test_vcf_merge: 307s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/Luz3rC8Wiv/merge.gvcf.3.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.3.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 307s .. ok 307s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.4.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.4.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.4.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.4.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.4.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.4.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.4.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.4.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.5.a.vcf.gz /tmp/Luz3rC8Wiv/merge.5.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.5.a.vcf.gz /tmp/Luz3rC8Wiv/merge.5.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.5.a.bcf /tmp/Luz3rC8Wiv/merge.5.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.5.a.bcf /tmp/Luz3rC8Wiv/merge.5.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.6.a.vcf.gz /tmp/Luz3rC8Wiv/merge.6.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.6.a.vcf.gz /tmp/Luz3rC8Wiv/merge.6.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.6.a.bcf /tmp/Luz3rC8Wiv/merge.6.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.6.a.bcf /tmp/Luz3rC8Wiv/merge.6.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.7.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.7.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.7.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.7.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.7.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.7.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.7.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.7.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.8.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.8.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.8.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.8.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.8.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.8.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.8.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.8.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples /tmp/Luz3rC8Wiv/merge.7.a.vcf.gz /tmp/Luz3rC8Wiv/merge.7.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples /tmp/Luz3rC8Wiv/merge.7.a.vcf.gz /tmp/Luz3rC8Wiv/merge.7.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --force-samples /tmp/Luz3rC8Wiv/merge.7.a.bcf /tmp/Luz3rC8Wiv/merge.7.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --force-samples /tmp/Luz3rC8Wiv/merge.7.a.bcf /tmp/Luz3rC8Wiv/merge.7.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9e.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9e.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9e.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9e.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9e.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9c.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9d.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.9e.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9e.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa -r 22:21-23 /tmp/Luz3rC8Wiv/merge.gvcf.9a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9c.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9d.bcf /tmp/Luz3rC8Wiv/merge.gvcf.9e.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.gvcf.10.fa -m none /tmp/Luz3rC8Wiv/merge.gvcf.10.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.noidx.a.vcf.gz /tmp/Luz3rC8Wiv/merge.noidx.b.vcf.gz /tmp/Luz3rC8Wiv/merge.noidx.c.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.noidx.a.vcf.gz /tmp/Luz3rC8Wiv/merge.noidx.b.vcf.gz /tmp/Luz3rC8Wiv/merge.noidx.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.noidx.a.bcf /tmp/Luz3rC8Wiv/merge.noidx.b.bcf /tmp/Luz3rC8Wiv/merge.noidx.c.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.noidx.a.bcf /tmp/Luz3rC8Wiv/merge.noidx.b.bcf /tmp/Luz3rC8Wiv/merge.noidx.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --no-index /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.noidx.a.vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.noidx.b.vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.noidx.c.vcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --no-index /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.noidx.a.vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.noidx.b.vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/merge.noidx.c.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --no-index /tmp/Luz3rC8Wiv/merge.noidx.a.bcf /tmp/Luz3rC8Wiv/merge.noidx.b.bcf /tmp/Luz3rC8Wiv/merge.noidx.c.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --no-index /tmp/Luz3rC8Wiv/merge.noidx.a.bcf /tmp/Luz3rC8Wiv/merge.noidx.b.bcf /tmp/Luz3rC8Wiv/merge.noidx.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.8.a.vcf.gz /tmp/Luz3rC8Wiv/merge.8.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.8.a.vcf.gz /tmp/Luz3rC8Wiv/merge.8.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.8.a.bcf /tmp/Luz3rC8Wiv/merge.8.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.8.a.bcf /tmp/Luz3rC8Wiv/merge.8.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.8.a.vcf.gz /tmp/Luz3rC8Wiv/merge.8.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.8.a.vcf.gz /tmp/Luz3rC8Wiv/merge.8.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.8.a.bcf /tmp/Luz3rC8Wiv/merge.8.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.8.a.bcf /tmp/Luz3rC8Wiv/merge.8.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.9.a.vcf.gz /tmp/Luz3rC8Wiv/merge.9.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.9.a.vcf.gz /tmp/Luz3rC8Wiv/merge.9.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version /tmp/Luz3rC8Wiv/merge.9.a.bcf /tmp/Luz3rC8Wiv/merge.9.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob /tmp/Luz3rC8Wiv/merge.9.a.bcf /tmp/Luz3rC8Wiv/merge.9.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.9.a.vcf.gz /tmp/Luz3rC8Wiv/merge.9.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.9.a.vcf.gz /tmp/Luz3rC8Wiv/merge.9.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.9.a.bcf /tmp/Luz3rC8Wiv/merge.9.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/Luz3rC8Wiv/merge.9.a.bcf /tmp/Luz3rC8Wiv/merge.9.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m none /tmp/Luz3rC8Wiv/merge.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.10.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m none /tmp/Luz3rC8Wiv/merge.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m none /tmp/Luz3rC8Wiv/merge.10.a.bcf /tmp/Luz3rC8Wiv/merge.10.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m none /tmp/Luz3rC8Wiv/merge.10.a.bcf /tmp/Luz3rC8Wiv/merge.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m both /tmp/Luz3rC8Wiv/merge.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.10.b.vcf.gz 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m both /tmp/Luz3rC8Wiv/merge.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m both /tmp/Luz3rC8Wiv/merge.10.a.bcf /tmp/Luz3rC8Wiv/merge.10.b.bcf 308s .. ok 308s 308s test_vcf_merge: 308s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m both /tmp/Luz3rC8Wiv/merge.10.a.bcf /tmp/Luz3rC8Wiv/merge.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m snp-ins-del /tmp/Luz3rC8Wiv/merge.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.10.b.vcf.gz 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m snp-ins-del /tmp/Luz3rC8Wiv/merge.10.a.vcf.gz /tmp/Luz3rC8Wiv/merge.10.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -m snp-ins-del /tmp/Luz3rC8Wiv/merge.10.a.bcf /tmp/Luz3rC8Wiv/merge.10.b.bcf 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob -m snp-ins-del /tmp/Luz3rC8Wiv/merge.10.a.bcf /tmp/Luz3rC8Wiv/merge.10.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.mrules.1.a.vcf.gz /tmp/Luz3rC8Wiv/merge.mrules.1.b.vcf.gz 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.mrules.1.a.vcf.gz /tmp/Luz3rC8Wiv/merge.mrules.1.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.mrules.1.a.bcf /tmp/Luz3rC8Wiv/merge.mrules.1.b.bcf 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.mrules.1.a.bcf /tmp/Luz3rC8Wiv/merge.mrules.1.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/Luz3rC8Wiv/merge.mrules.1.a.vcf.gz /tmp/Luz3rC8Wiv/merge.mrules.1.b.vcf.gz 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/Luz3rC8Wiv/merge.mrules.1.a.vcf.gz /tmp/Luz3rC8Wiv/merge.mrules.1.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/Luz3rC8Wiv/merge.mrules.1.a.bcf /tmp/Luz3rC8Wiv/merge.mrules.1.b.bcf 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/Luz3rC8Wiv/merge.mrules.1.a.bcf /tmp/Luz3rC8Wiv/merge.mrules.1.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.5.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.5.b.vcf.gz 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.5.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.5.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.5.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.5.b.bcf 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.5.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.5.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - --merge none /tmp/Luz3rC8Wiv/merge.gvcf.5.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.5.b.vcf.gz 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/Luz3rC8Wiv/merge.gvcf.5.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.5.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - --merge none /tmp/Luz3rC8Wiv/merge.gvcf.5.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.5.b.bcf 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/Luz3rC8Wiv/merge.gvcf.5.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.5.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.11.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.11.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.11.c.vcf.gz 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.11.a.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.11.b.vcf.gz /tmp/Luz3rC8Wiv/merge.gvcf.11.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.11.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.11.b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.11.c.bcf 309s .. ok 309s 309s test_vcf_merge: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools merge --no-version -Ob --gvcf - /tmp/Luz3rC8Wiv/merge.gvcf.11.a.bcf /tmp/Luz3rC8Wiv/merge.gvcf.11.b.bcf /tmp/Luz3rC8Wiv/merge.gvcf.11.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version | grep -v ^##bcftools_ 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/Luz3rC8Wiv/query.string.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.string.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/Luz3rC8Wiv/query.string.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.string.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/Luz3rC8Wiv/query.string.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.string.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.string.2.1.txt' /tmp/Luz3rC8Wiv/query.string.2.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.string.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.string.2.1.txt' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.string.2.2.txt' /tmp/Luz3rC8Wiv/query.string.2.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.string.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.string.2.2.txt' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%RSX\t%VKX\n' /tmp/Luz3rC8Wiv/query.variantkey.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.variantkey.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%RSX\t%VKX\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XRI\n' -i'XRI[*]>1111' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/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/Luz3rC8Wiv/view.vectors.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.vectors.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/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' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/Luz3rC8Wiv/query.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/Luz3rC8Wiv/query.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/Luz3rC8Wiv/query.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/Luz3rC8Wiv/query.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/Luz3rC8Wiv/query.2.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IINT="."' -f'%POS %IINT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IINT!="."' -f'%POS %IINT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IINT!="."' -f'%POS %IINT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IINT="."' -f'%POS %IINT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/Luz3rC8Wiv/filter.11.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/Luz3rC8Wiv/filter.11.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/Luz3rC8Wiv/filter.11.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/Luz3rC8Wiv/filter.11.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%LINE' /tmp/Luz3rC8Wiv/query.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%LINE' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter-type.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/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/Luz3rC8Wiv/filter-missing-floats.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter-missing-floats.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/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' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/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/Luz3rC8Wiv/filter-missing-floats.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter-missing-floats.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/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' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/Luz3rC8Wiv/missing.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/Luz3rC8Wiv/query.filter.2.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/Luz3rC8Wiv/filter.5.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/Luz3rC8Wiv/filter.5.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.filter.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/Luz3rC8Wiv/query.filter.3.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/Luz3rC8Wiv/query.filter.3.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/Luz3rC8Wiv/query.filter.3.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/Luz3rC8Wiv/filter.5.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/Luz3rC8Wiv/query.filter.4.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%ID\n' -i 'ID=@/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.56.out' /tmp/Luz3rC8Wiv/view.vcf.gz 309s .. ok 309s 309s test_vcf_query: 309s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%ID\n' -i 'ID=@/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.56.out' 309s .. ok 309s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/Luz3rC8Wiv/query.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/Luz3rC8Wiv/query.negative.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.negative.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/Luz3rC8Wiv/query.negative.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.negative.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/Luz3rC8Wiv/query.negative.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.negative.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/Luz3rC8Wiv/query.negative.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.negative.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/Luz3rC8Wiv/query.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/Luz3rC8Wiv/query.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/Luz3rC8Wiv/query.filter.6.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.6.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.7.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/Luz3rC8Wiv/query.filter.8.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.8.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/Luz3rC8Wiv/query.filter.8.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.8.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/Luz3rC8Wiv/query.filter.9.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.9.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/Luz3rC8Wiv/query.filter.9.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.9.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/Luz3rC8Wiv/query.filter.13.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.13.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/Luz3rC8Wiv/query.filter.10.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.10.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/Luz3rC8Wiv/query.filter.10.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.10.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/Luz3rC8Wiv/query.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/Luz3rC8Wiv/query.filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/Luz3rC8Wiv/query.filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt /tmp/Luz3rC8Wiv/query.smpl.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.smpl.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -l -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt /tmp/Luz3rC8Wiv/query.smpl.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.smpl.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -l -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f "[%SAMPLE %GT\n]" -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt /tmp/Luz3rC8Wiv/query.smpl.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.smpl.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f "[%SAMPLE %GT\n]" -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -l -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt /tmp/Luz3rC8Wiv/query.smpl.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.smpl.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -l -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.11.txt 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.txt /tmp/Luz3rC8Wiv/query.smpl.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.smpl.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.txt 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -l -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.txt /tmp/Luz3rC8Wiv/query.smpl.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.smpl.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -l -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/query.smpl.txt 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/Luz3rC8Wiv/query.filter.id.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.id.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%ID\n' -i'ID~"s12"' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/Luz3rC8Wiv/query.filter.id.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.filter.id.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%ID\n' -i'ID="rs123"' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/Luz3rC8Wiv/filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="A"' -f'%FILTER\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/Luz3rC8Wiv/filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER~"A"' -f'%FILTER\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/Luz3rC8Wiv/filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/Luz3rC8Wiv/filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/Luz3rC8Wiv/filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/Luz3rC8Wiv/filter.12.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.12.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/Luz3rC8Wiv/filter.10.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.10.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'DP%10==2' -f'[ %DP]\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/Luz3rC8Wiv/filter.13.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/filter.13.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/Luz3rC8Wiv/query.header.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.header.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/Luz3rC8Wiv/query.header.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.header.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/Luz3rC8Wiv/query.header.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.header.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/Luz3rC8Wiv/query.header.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.header.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/Luz3rC8Wiv/query.header.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.header.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/Luz3rC8Wiv/query.header.vcf.gz 310s .. ok 310s 310s test_vcf_query: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/query.header.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -cx -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -cx -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m- /tmp/Luz3rC8Wiv/norm.split.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m- /tmp/Luz3rC8Wiv/norm.split.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m- /tmp/Luz3rC8Wiv/norm.split.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m- /tmp/Luz3rC8Wiv/norm.split.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m- --force /tmp/Luz3rC8Wiv/norm.split.3.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m- --force /tmp/Luz3rC8Wiv/norm.split.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m- /tmp/Luz3rC8Wiv/norm.split.4.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m- /tmp/Luz3rC8Wiv/norm.split.4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m- --keep-sum AD /tmp/Luz3rC8Wiv/norm.split.4.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m- --keep-sum AD /tmp/Luz3rC8Wiv/norm.split.4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m- -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.split.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m- -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.split.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m+ /tmp/Luz3rC8Wiv/norm.merge.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m+ /tmp/Luz3rC8Wiv/norm.merge.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m+ /tmp/Luz3rC8Wiv/norm.merge.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m+ /tmp/Luz3rC8Wiv/norm.merge.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m+ /tmp/Luz3rC8Wiv/norm.merge.3.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m+ /tmp/Luz3rC8Wiv/norm.merge.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m+ -s /tmp/Luz3rC8Wiv/norm.merge.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m+ -s /tmp/Luz3rC8Wiv/norm.merge.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -Nc s -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.setref.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -Nc s -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.setref.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.telomere.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.fa /tmp/Luz3rC8Wiv/norm.telomere.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d snps /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d snps /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d indels /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d indels /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d both /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d both /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d all /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d all /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d none /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d none /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d exact /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d exact /tmp/Luz3rC8Wiv/norm.rmdup.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d none /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d none /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d exact /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d exact /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d indels /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d indels /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d any /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d any /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d both /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d both /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -d snps /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -d snps /tmp/Luz3rC8Wiv/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -c s -a -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.2.fa /tmp/Luz3rC8Wiv/norm.2.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -c s -a -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.2.fa /tmp/Luz3rC8Wiv/norm.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -c s -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.iupac.fa /tmp/Luz3rC8Wiv/norm.iupac.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -c s -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.iupac.fa /tmp/Luz3rC8Wiv/norm.iupac.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -c s -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.3.fa /tmp/Luz3rC8Wiv/norm.3.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -c s -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.3.fa /tmp/Luz3rC8Wiv/norm.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --old-rec-tag OLD_REC -m -any /tmp/Luz3rC8Wiv/atomize.split.1.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --old-rec-tag OLD_REC -m -any /tmp/Luz3rC8Wiv/atomize.split.1.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.1.vcf.gz 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.1.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 310s .. ok 310s 310s test_vcf_norm: 310s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.1.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.1.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.2.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.2.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --atom-overlaps . /tmp/Luz3rC8Wiv/atomize.split.3.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --atom-overlaps . /tmp/Luz3rC8Wiv/atomize.split.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.4.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/Luz3rC8Wiv/atomize.split.4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m +both /tmp/Luz3rC8Wiv/norm.4.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m +both /tmp/Luz3rC8Wiv/norm.4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m +any /tmp/Luz3rC8Wiv/norm.4.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m +any /tmp/Luz3rC8Wiv/norm.4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/Luz3rC8Wiv/norm.5.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m - --multi-overlaps 0 /tmp/Luz3rC8Wiv/norm.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m - --multi-overlaps . /tmp/Luz3rC8Wiv/norm.5.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m - --multi-overlaps . /tmp/Luz3rC8Wiv/norm.5.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m -any /tmp/Luz3rC8Wiv/norm.m-any.vcf.gz 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m -any /tmp/Luz3rC8Wiv/norm.m-any.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 311s .. ok 311s 311s test_vcf_norm: 311s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m -any /tmp/Luz3rC8Wiv/norm.phased-split.vcf.gz 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m -any /tmp/Luz3rC8Wiv/norm.phased-split.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version -m +any /tmp/Luz3rC8Wiv/norm.phased-join.vcf.gz 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob -m +any /tmp/Luz3rC8Wiv/norm.phased-join.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --old-rec-tag ORI -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.symbolic.fa /tmp/Luz3rC8Wiv/norm.symbolic.vcf.gz 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --old-rec-tag ORI -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.symbolic.fa /tmp/Luz3rC8Wiv/norm.symbolic.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --old-rec-tag ORI -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.symbolic.fa /tmp/Luz3rC8Wiv/norm.symbolic.2.vcf.gz 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --old-rec-tag ORI -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.symbolic.fa /tmp/Luz3rC8Wiv/norm.symbolic.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --old-rec-tag ORI -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.right-align.fa /tmp/Luz3rC8Wiv/norm.right-align.vcf.gz 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --old-rec-tag ORI -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.right-align.fa /tmp/Luz3rC8Wiv/norm.right-align.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm --no-version --old-rec-tag ORI -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.right-align.gff -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.right-align.fa /tmp/Luz3rC8Wiv/norm.right-align.vcf.gz 312s .. ok 312s 312s test_vcf_norm: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools norm -Ob --old-rec-tag ORI -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.right-align.gff -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/norm.right-align.fa /tmp/Luz3rC8Wiv/norm.right-align.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -HA /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -HAA /tmp/Luz3rC8Wiv/merge.gvcf.2.a.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1:1-2 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1:1-2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1:1,1:2 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1:1,1:2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1:1-1 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r 1:1-1 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1} 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1} | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1}:1-2 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1}:1-2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1}:1-1 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1}:1-1 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1} 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1} | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}:1-2 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}:1-1 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}-2 312s .. ok, expected non-zero status 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/weird-chr-names.vcf.gz -r {1:1-1}-2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok, expected non-zero status 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -f PASS -Xks NA00003 /tmp/Luz3rC8Wiv/view.vcf.gz -r20,Y 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -f PASS -Xks NA00003 /tmp/Luz3rC8Wiv/view.vcf.gz -r20,Y | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -xs NA00003 /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -xs NA00003 /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -p /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -p /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -P /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -P /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -Hu /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -GVsnps /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -GVsnps /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -s ^NA00003 /tmp/Luz3rC8Wiv/view.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -s ^NA00003 /tmp/Luz3rC8Wiv/view.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version /tmp/Luz3rC8Wiv/view.omitgenotypes.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/view.omitgenotypes.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -G /tmp/Luz3rC8Wiv/view.omitgenotypes.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -G /tmp/Luz3rC8Wiv/view.omitgenotypes.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -HG /tmp/Luz3rC8Wiv/view.omitgenotypes.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -a /tmp/Luz3rC8Wiv/many.alleles.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -a /tmp/Luz3rC8Wiv/many.alleles.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -asA /tmp/Luz3rC8Wiv/view.vectors.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -asA /tmp/Luz3rC8Wiv/view.vectors.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -asB /tmp/Luz3rC8Wiv/view.vectors.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -asB /tmp/Luz3rC8Wiv/view.vectors.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -asA /tmp/Luz3rC8Wiv/view.vectors.2.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -asA /tmp/Luz3rC8Wiv/view.vectors.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i'TXT0="text"' /tmp/Luz3rC8Wiv/view.filter.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.chrs.tab /tmp/Luz3rC8Wiv/view.chrs.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.chrs.tab /tmp/Luz3rC8Wiv/view.chrs.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -i 'POS>=3062917' /tmp/Luz3rC8Wiv/filter.2.vcf.gz 1:3062917-3157410 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -i 'POS>=3062917' /tmp/Luz3rC8Wiv/filter.2.vcf.gz 1:3062917-3157410 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/Luz3rC8Wiv/idx.1.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/Luz3rC8Wiv/idx.2.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/idx.2.bed /tmp/Luz3rC8Wiv/idx.2.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/idx.3.bed /tmp/Luz3rC8Wiv/idx.3.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/idx.4.bed /tmp/Luz3rC8Wiv/idx.4.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -Ht 2 /tmp/Luz3rC8Wiv/view-t.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -Ht 3 /tmp/Luz3rC8Wiv/view-t.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/Luz3rC8Wiv/overlap.vcf.gz 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.1.vcf -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.1.vcf -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.2.vcf -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.2.vcf -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.3.vcf -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.4.vcf -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.4.vcf -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.5.vcf -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_64bit: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view64bit.5.vcf -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -C5:nonmajor /tmp/Luz3rC8Wiv/view.minmaxac.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -c6:nonmajor /tmp/Luz3rC8Wiv/view.minmaxac.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -q0.3:major /tmp/Luz3rC8Wiv/view.minmaxac.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/Luz3rC8Wiv/view.filter.annovar.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/Luz3rC8Wiv/view.filter.annovar.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/Luz3rC8Wiv/view.filter.annovar.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -H -a /tmp/Luz3rC8Wiv/view-a.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.sites.txt /tmp/Luz3rC8Wiv/view.sites.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.sites.txt /tmp/Luz3rC8Wiv/view.sites.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.sites.txt.gz /tmp/Luz3rC8Wiv/view.sites.vcf.gz 312s .. ok 312s 312s test_vcf_view: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.sites.txt.gz /tmp/Luz3rC8Wiv/view.sites.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -h 0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -h 1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -h 5 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -h 22 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -h 23 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -n 0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -n 1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -n 5 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -h 5 -n 5 < /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_head2: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -s0 /tmp/Luz3rC8Wiv/mpileup.2.vcf.gz 312s .. ok 312s 312s test_vcf_head2: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -Ob /tmp/Luz3rC8Wiv/mpileup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -s0 312s .. ok 312s 312s test_vcf_head2: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -s1 /tmp/Luz3rC8Wiv/mpileup.2.vcf.gz 312s .. ok 312s 312s test_vcf_head2: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -Ob /tmp/Luz3rC8Wiv/mpileup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -s1 312s .. ok 312s 312s test_vcf_head2: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -s2 -h2 /tmp/Luz3rC8Wiv/mpileup.2.vcf.gz 312s .. ok 312s 312s test_vcf_head2: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version -Ob /tmp/Luz3rC8Wiv/mpileup.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools head -s2 -h2 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mg0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mg0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.4.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.4.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.5.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.5.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.X.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.X.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ped /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.X.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ped /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.X.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.X.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.X.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.NA19213.NA19129.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.NA19213.NA19129.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.NA19213.NA19129.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.NA19213.NA19129.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.samples --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.samples --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.2.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.2.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.3.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.3.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.4.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.4.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.5.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.5.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.6.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.4.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.6.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.7.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.5.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.7.tab.gz -i /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.cals.1.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.cals.1.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.cals.1.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.cals.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.cals.2.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.cals.2.vcf 312s .. ok 312s 312s test_vcf_call_cAls: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mA -C alleles -T /tmp/Luz3rC8Wiv/mpileup.cals.2.tab.gz /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.cals.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -cv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -cv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.X.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ped /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.X.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ped /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.X.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.ploidy -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.2.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call-G.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call-G.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call-G.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call-G.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -mv -F AN_POP,AC_POP /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call-G.2.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -mv -F AN_POP,AC_POP /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call-G.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -m -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.txt /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -m -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.txt /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call --no-version -m -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.txt -a GP,GQ /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.vcf 312s .. ok 312s 312s test_vcf_call: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools call -Ob -m -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.txt -a GP,GQ /tmp/autopkgtest.ig2rlO/build.E6f/src/test/call.af-fixation.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'TXT0="text"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'TXT0="text"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'FMT/STR="XX"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'FMT/STR="XX"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S. -e'FMT/FILTER="aaa"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.2.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/view.filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -mx -g2 -G2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -mx -g2 -G2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'INFO/DP=19' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'INFO/DP=19' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'INFO/DP=19' -s XX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'INFO/DP=19' -s XX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'INFO/DP=19' -s XX -m+ /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'INFO/DP=19' -s XX -mx /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'INFO/DP=19' -s XX -m+x /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'FMT/GT="0/2"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'FMT/GT="0/2"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'FMT/GT="0/2"' -s XX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%AC[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%AC[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%AC[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%AC[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'ALT="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%AC[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'ALT="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%AC[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -i 'FORMAT/TEST3<25' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.4.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -i 'FORMAT/TEST4<25' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.4.vcf | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="A"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="A"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="RR"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="RR"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="RA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="RA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="AR"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="AR"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="AA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="AA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="aA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="aA"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="Aa"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="Aa"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="HOM"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="HOM"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="HET"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="HET"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'GT="HAP"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'GT="HAP"' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%GT]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'AD[:1]=11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'AD[:1]=11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'AD[1:]=11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'AD[1:]=11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'FR[0:1]=11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%FR]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'FR[0:1]=11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%FR]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'AD[*]="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'AD[*]="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'AD[0:0]=="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'AD[0:0]=="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'AD[0:0]!="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'AD[0:0]!="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS[\t%AD]\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'QUAL=="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%QUAL\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'QUAL=="."' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\t%QUAL\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'N_PASS(DP>32)=1' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'N_PASS(DP>32)=1' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'F_PASS(DP>32)=0.5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'F_MISSING>=1/5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'F_MISSING>=1/5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'F_MISSING>=0.2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'F_MISSING>=0.2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 312s .. ok 312s 312s test_vcf_filter: 312s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%POS\n' 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -mx -s + -g2:mnp,indel,other /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.7.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.7.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'FORMAT/AO==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i 'QUAL/FMT/AD==55' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.9.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.9.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i 'QUAL/INFO/AD==10' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.9.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.9.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -S . -e 'ABS(AO[1:])==2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.10.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_filter: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/filter.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_sort: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools sort -m 0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/sort.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' 313s .. ok 313s 313s test_vcf_sort: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools sort -Ob -m 0 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/sort.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' 313s .. ok 313s 313s test_vcf_sort: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools sort -m 1000 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/sort.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' 313s .. ok 313s 313s test_vcf_sort: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools sort -Ob -m 1000 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/sort.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/regions.tab /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/regions.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/autopkgtest.ig2rlO/build.E6f/src/test/regions.tab 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/autopkgtest.ig2rlO/build.E6f/src/test/regions.tab /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Luz3rC8Wiv/regions.tab.gz /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/regions.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Luz3rC8Wiv/regions.tab.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Luz3rC8Wiv/regions.tab.gz /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Luz3rC8Wiv/regions.bed /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/regions.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Luz3rC8Wiv/regions.bed 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Luz3rC8Wiv/regions.bed /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Luz3rC8Wiv/regions.bed.gz /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/regions.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/Luz3rC8Wiv/regions.bed.gz 313s .. ok 313s 313s test_vcf_regions: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/Luz3rC8Wiv/regions.bed.gz /tmp/Luz3rC8Wiv/regions.vcf.gz 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate2.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.hdr -c CHROM,POS,-,T_STR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate2.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.hdr -c CHROM,POS,-,T_STR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate2.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.hdr -c CHROM,FROM,TO,T_STR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate2.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.hdr -c CHROM,FROM,TO,T_STR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/Luz3rC8Wiv/annotate.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/Luz3rC8Wiv/annotate.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -x FORMAT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -x FORMAT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots4.vcf.gz -c +INFO /tmp/Luz3rC8Wiv/annotate4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots4.vcf.gz -c +INFO /tmp/Luz3rC8Wiv/annotate4.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots4.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots4.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots10.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate10.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots10.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate10.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots11.vcf.gz -c FMT /tmp/Luz3rC8Wiv/annotate11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots11.vcf.gz -c FMT /tmp/Luz3rC8Wiv/annotate11.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c FMT/newGT:=GT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots2.vcf.gz -c FMT/newGT:=GT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots12.vcf.gz -c FMT/GT:=newGT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots12.vcf.gz -c FMT/GT:=newGT /tmp/Luz3rC8Wiv/annotate2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots13.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.hdr -c CHROM,BEG,END,ABC /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots13.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.hdr -c CHROM,BEG,END,ABC /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots13.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots13.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots13.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots13.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate13.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -x FILTER/XX,INFO/XX --force /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate14.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate14.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate15.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate15.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate15.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate15.tab.gz -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate15.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -x FILTER /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate16.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -x FILTER /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate16.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate17.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate17.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate17.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate17.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate17.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate17.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate18.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate18.1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate18.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate18.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 313s .. ok 313s 313s test_vcf_annotate: 313s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -c INFO/FILTER:=FILTER /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate19.dst.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -c INFO/FILTER:=FILTER /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate19.dst.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/Luz3rC8Wiv/annotate19.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate20.src.vcf.gz -c FMT/GT /tmp/Luz3rC8Wiv/annotate20.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate20.src.vcf.gz -c FMT/GT /tmp/Luz3rC8Wiv/annotate20.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate20.src.vcf.gz -c +FMT/GT /tmp/Luz3rC8Wiv/annotate20.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate20.src.vcf.gz -c +FMT/GT /tmp/Luz3rC8Wiv/annotate20.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate20.src.vcf.gz -c -FMT/GT /tmp/Luz3rC8Wiv/annotate20.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate20.src.vcf.gz -c -FMT/GT /tmp/Luz3rC8Wiv/annotate20.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.multi.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.multi.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing-append.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing-append.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate9.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate9.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate --rename-annots /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate21.txt /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate21.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob --rename-annots /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate21.txt /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate21.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/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 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate21.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/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 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate21.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/Luz3rC8Wiv/annotate22.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/Luz3rC8Wiv/annotate22.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate23.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate23.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate24.src.vcf.gz -c XX /tmp/Luz3rC8Wiv/annotate24.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate24.src.vcf.gz -c XX /tmp/Luz3rC8Wiv/annotate24.dst.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate25.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate25.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate26.tab.gz -c CHROM,POS,~POS /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate26.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate26.tab.gz -c CHROM,POS,~POS /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate26.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.missing.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.olap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.olap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.olap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.olap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.id.vcf.gz -c ALT /tmp/Luz3rC8Wiv/annotate.id.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.id.vcf.gz -c ALT /tmp/Luz3rC8Wiv/annotate.id.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.id.vcf.gz -c +ALT /tmp/Luz3rC8Wiv/annotate.id.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.id.vcf.gz -c +ALT /tmp/Luz3rC8Wiv/annotate.id.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/Luz3rC8Wiv/annotate.id.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/Luz3rC8Wiv/annotate.id.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/Luz3rC8Wiv/annotate.id.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/Luz3rC8Wiv/annotate.id.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate27.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate27.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate28.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -m XXX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -m XXX /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate34.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate34.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -a /tmp/Luz3rC8Wiv/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annots-mark.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_annotate: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate -Ob -a /tmp/Luz3rC8Wiv/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annots-mark.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version /tmp/Luz3rC8Wiv/concat.1.a.vcf.gz /tmp/Luz3rC8Wiv/concat.1.b.vcf.gz 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob /tmp/Luz3rC8Wiv/concat.1.a.vcf.gz /tmp/Luz3rC8Wiv/concat.1.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version /tmp/Luz3rC8Wiv/concat.1.a.bcf /tmp/Luz3rC8Wiv/concat.1.b.bcf 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob /tmp/Luz3rC8Wiv/concat.1.a.bcf /tmp/Luz3rC8Wiv/concat.1.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -a /tmp/Luz3rC8Wiv/concat.2.a.vcf.gz /tmp/Luz3rC8Wiv/concat.2.b.vcf.gz 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -a /tmp/Luz3rC8Wiv/concat.2.a.vcf.gz /tmp/Luz3rC8Wiv/concat.2.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -a /tmp/Luz3rC8Wiv/concat.2.a.bcf /tmp/Luz3rC8Wiv/concat.2.b.bcf 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -a /tmp/Luz3rC8Wiv/concat.2.a.bcf /tmp/Luz3rC8Wiv/concat.2.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -aD /tmp/Luz3rC8Wiv/concat.2.a.vcf.gz /tmp/Luz3rC8Wiv/concat.2.b.vcf.gz 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -aD /tmp/Luz3rC8Wiv/concat.2.a.vcf.gz /tmp/Luz3rC8Wiv/concat.2.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -aD /tmp/Luz3rC8Wiv/concat.2.a.bcf /tmp/Luz3rC8Wiv/concat.2.b.bcf 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -aD /tmp/Luz3rC8Wiv/concat.2.a.bcf /tmp/Luz3rC8Wiv/concat.2.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l --ligate-warn /tmp/Luz3rC8Wiv/concat.3.a.vcf.gz /tmp/Luz3rC8Wiv/concat.3.b.vcf.gz /tmp/Luz3rC8Wiv/concat.3.0.vcf.gz /tmp/Luz3rC8Wiv/concat.3.c.vcf.gz /tmp/Luz3rC8Wiv/concat.3.d.vcf.gz /tmp/Luz3rC8Wiv/concat.3.e.vcf.gz /tmp/Luz3rC8Wiv/concat.3.f.vcf.gz 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l --ligate-warn /tmp/Luz3rC8Wiv/concat.3.a.vcf.gz /tmp/Luz3rC8Wiv/concat.3.b.vcf.gz /tmp/Luz3rC8Wiv/concat.3.0.vcf.gz /tmp/Luz3rC8Wiv/concat.3.c.vcf.gz /tmp/Luz3rC8Wiv/concat.3.d.vcf.gz /tmp/Luz3rC8Wiv/concat.3.e.vcf.gz /tmp/Luz3rC8Wiv/concat.3.f.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l --ligate-warn /tmp/Luz3rC8Wiv/concat.3.a.bcf /tmp/Luz3rC8Wiv/concat.3.b.bcf /tmp/Luz3rC8Wiv/concat.3.0.bcf /tmp/Luz3rC8Wiv/concat.3.c.bcf /tmp/Luz3rC8Wiv/concat.3.d.bcf /tmp/Luz3rC8Wiv/concat.3.e.bcf /tmp/Luz3rC8Wiv/concat.3.f.bcf 314s .. ok 314s 314s test_vcf_concat: 314s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l --ligate-warn /tmp/Luz3rC8Wiv/concat.3.a.bcf /tmp/Luz3rC8Wiv/concat.3.b.bcf /tmp/Luz3rC8Wiv/concat.3.0.bcf /tmp/Luz3rC8Wiv/concat.3.c.bcf /tmp/Luz3rC8Wiv/concat.3.d.bcf /tmp/Luz3rC8Wiv/concat.3.e.bcf /tmp/Luz3rC8Wiv/concat.3.f.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 314s Random seed for test_naive_concat: 1504634924 314s .. ok 314s 315s test_naive_concat: 315s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --naive-force /tmp/Luz3rC8Wiv/naive_concat.0.bcf /tmp/Luz3rC8Wiv/naive_concat.1.bcf /tmp/Luz3rC8Wiv/naive_concat.2.bcf /tmp/Luz3rC8Wiv/naive_concat.3.bcf /tmp/Luz3rC8Wiv/naive_concat.4.bcf /tmp/Luz3rC8Wiv/naive_concat.5.bcf /tmp/Luz3rC8Wiv/naive_concat.6.bcf /tmp/Luz3rC8Wiv/naive_concat.7.bcf /tmp/Luz3rC8Wiv/naive_concat.8.bcf /tmp/Luz3rC8Wiv/naive_concat.9.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 315s .. ok 315s 315s test_naive_concat: 315s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --naive /tmp/Luz3rC8Wiv/naive_concat.0.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.1.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.2.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.3.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.4.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.5.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.6.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.7.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.8.vcf.gz /tmp/Luz3rC8Wiv/naive_concat.9.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -H 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l /tmp/Luz3rC8Wiv/concat.4.a.vcf.gz /tmp/Luz3rC8Wiv/concat.4.b.vcf.gz 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l /tmp/Luz3rC8Wiv/concat.4.a.vcf.gz /tmp/Luz3rC8Wiv/concat.4.b.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l /tmp/Luz3rC8Wiv/concat.4.a.bcf /tmp/Luz3rC8Wiv/concat.4.b.bcf 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l /tmp/Luz3rC8Wiv/concat.4.a.bcf /tmp/Luz3rC8Wiv/concat.4.b.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l --ligate-warn /tmp/Luz3rC8Wiv/concat.5.a.vcf.gz /tmp/Luz3rC8Wiv/concat.5.b.vcf.gz /tmp/Luz3rC8Wiv/concat.5.c.vcf.gz 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l --ligate-warn /tmp/Luz3rC8Wiv/concat.5.a.vcf.gz /tmp/Luz3rC8Wiv/concat.5.b.vcf.gz /tmp/Luz3rC8Wiv/concat.5.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l --ligate-warn /tmp/Luz3rC8Wiv/concat.5.a.bcf /tmp/Luz3rC8Wiv/concat.5.b.bcf /tmp/Luz3rC8Wiv/concat.5.c.bcf 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l --ligate-warn /tmp/Luz3rC8Wiv/concat.5.a.bcf /tmp/Luz3rC8Wiv/concat.5.b.bcf /tmp/Luz3rC8Wiv/concat.5.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -l --ligate-force /tmp/Luz3rC8Wiv/concat.5.a.bcf /tmp/Luz3rC8Wiv/concat.5.b.bcf /tmp/Luz3rC8Wiv/concat.5.c.bcf 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -l --ligate-force /tmp/Luz3rC8Wiv/concat.5.a.bcf /tmp/Luz3rC8Wiv/concat.5.b.bcf /tmp/Luz3rC8Wiv/concat.5.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -G -a -D /tmp/Luz3rC8Wiv/concat.5.a.vcf.gz /tmp/Luz3rC8Wiv/concat.5.b.vcf.gz /tmp/Luz3rC8Wiv/concat.5.c.vcf.gz 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -G -a -D /tmp/Luz3rC8Wiv/concat.5.a.vcf.gz /tmp/Luz3rC8Wiv/concat.5.b.vcf.gz /tmp/Luz3rC8Wiv/concat.5.c.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat --no-version -G -a -D /tmp/Luz3rC8Wiv/concat.5.a.bcf /tmp/Luz3rC8Wiv/concat.5.b.bcf /tmp/Luz3rC8Wiv/concat.5.c.bcf 316s .. ok 316s 316s test_vcf_concat: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools concat -Ob -G -a -D /tmp/Luz3rC8Wiv/concat.5.a.bcf /tmp/Luz3rC8Wiv/concat.5.b.bcf /tmp/Luz3rC8Wiv/concat.5.c.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.hdr /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.hdr | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.hdr /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.hdr | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.hdr /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.hdr | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples2 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples2 /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples2 /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples2 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples3 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples3 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples3 /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples3 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples3 /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples3 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples4 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples4 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples4 /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples4 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples4 /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/reheader.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -s /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.samples4 | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.empty.hdr /tmp/autopkgtest.ig2rlO/build.E6f/src/test/empty.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/autopkgtest.ig2rlO/build.E6f/src/test/empty.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.empty.hdr | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.empty.hdr /tmp/Luz3rC8Wiv/empty.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/empty.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.empty.hdr | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.empty.hdr /tmp/Luz3rC8Wiv/empty.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s cat /tmp/Luz3rC8Wiv/empty.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.empty.hdr | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.fai /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.fai /tmp/Luz3rC8Wiv/reheader.2.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.fai /tmp/Luz3rC8Wiv/reheader.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.2.hdr -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.fai /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.2.hdr -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.fai /tmp/Luz3rC8Wiv/reheader.2.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -h /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.2.hdr -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.fai /tmp/Luz3rC8Wiv/reheader.2.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.3.fai /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.3.fai /tmp/Luz3rC8Wiv/reheader.3.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_vcf_reheader: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools reheader -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/reheader.3.fai /tmp/Luz3rC8Wiv/reheader.3.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view --no-version 316s .. ok 316s 316s test_rename_chrs: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate --rename-chrs /tmp/Luz3rC8Wiv/rename.map -Ov /tmp/Luz3rC8Wiv/annotate.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM\t%POS\n' 316s .. ok 316s 316s test_rename_chrs: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate --rename-chrs /tmp/Luz3rC8Wiv/rename.map -Ob /tmp/Luz3rC8Wiv/annotate.bcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM\t%POS\n' 316s .. ok 316s 316s test_rename_chrs: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate --rename-chrs /tmp/Luz3rC8Wiv/rename.map -Ov /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM\t%POS\n' 316s .. ok 316s 316s test_rename_chrs: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools annotate --rename-chrs /tmp/Luz3rC8Wiv/rename.map -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/annotate.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%CHROM\t%POS\n' 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --vcf-ids /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --vcf-ids --3N6 /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --vcf-ids --3N6 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --3N6 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.3N6.gen,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --3N6 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.3N6.gen,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --tag PL /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --tag PL 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --tag PL /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --tag PL 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --vcf-ids /tmp/Luz3rC8Wiv/check.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --vcf-ids /tmp/Luz3rC8Wiv/check.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --3N6 /tmp/Luz3rC8Wiv/check.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --3N6 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --3N6 /tmp/Luz3rC8Wiv/check.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --3N6 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --3N6 --vcf-ids /tmp/Luz3rC8Wiv/check.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g -,. --3N6 --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --3N6 --vcf-ids /tmp/Luz3rC8Wiv/check.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/check.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -g .,- --3N6 --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h -,.,. /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h -,.,. 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h .,-,. /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h .,-,. 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h .,-,. --vcf-ids /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h .,-,. --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h .,.,- /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -h .,.,- 316s .. ok 316s 316s test_vcf_convert_hls2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -H /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hls.gt.hap,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hls.gt.legend,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hls.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hls2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -H /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hls.gt.hap,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hls.gt.legend,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hls.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --haplegendsample -,.,. /tmp/Luz3rC8Wiv/convert.hap-missing.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.hap-missing.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --haplegendsample -,.,. 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample -,. /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample -,. 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample -,. --vcf-ids /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample -,. --vcf-ids 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample .,- /tmp/Luz3rC8Wiv/convert.vcf.gz 316s .. ok 316s 316s test_vcf_convert: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample .,- 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.hap,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --hapsample2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.hap,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --vcf-ids --hapsample2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.ids.hap,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.samples | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_hs2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --vcf-ids --hapsample2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.ids.hap,/tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.hs.gt.samples -Ou | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^## 316s .. ok 316s 316s test_vcf_convert_gvcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa /tmp/Luz3rC8Wiv/convert.gvcf.vcf.gz 316s .. ok 316s 316s test_vcf_convert_gvcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view -Ob /tmp/Luz3rC8Wiv/convert.gvcf.vcf.gz | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gvcf.fa | grep -v ^##bcftools 316s .. ok 316s 316s test_vcf_convert_tsv2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.23andme 316s .. ok 316s 316s test_vcf_convert_tsv2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.23andme | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_convert_tsv2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.tsv 316s .. ok 316s 316s test_vcf_convert_tsv2vcf: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.ig2rlO/build.E6f/src/test/convert.tsv | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools_ 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab 316s .. ok 316s 316s test_vcf_consensus_chain: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab -c /tmp/Luz3rC8Wiv/consensus.1.chain.new >/dev/null; cat /tmp/Luz3rC8Wiv/consensus.1.chain.new 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab 316s .. ok 316s 316s test_vcf_consensus_chain: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab -c /tmp/Luz3rC8Wiv/consensus.2.chain.new >/dev/null; cat /tmp/Luz3rC8Wiv/consensus.2.chain.new 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -I -s - -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -I -s - -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -I -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab --mask-with X -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab --mask-with lc 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -I -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab --mask-with X -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab --mask-with lc 316s .. ok 316s 316s test_vcf_consensus_chain: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -I -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.tab -c /tmp/Luz3rC8Wiv/consensus.3.chain.new >/dev/null; cat /tmp/Luz3rC8Wiv/consensus.3.chain.new 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H 1 316s .. ok 316s 316s test_vcf_consensus: 316s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H 1 317s .. ok 317s 317s test_vcf_consensus_chain: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H 1 -c /tmp/Luz3rC8Wiv/consensus.4.chain.new >/dev/null; cat /tmp/Luz3rC8Wiv/consensus.4.chain.new 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus2.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 1 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus2.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 1 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus2.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 2 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus2.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 2 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/empty.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/empty.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus3.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 2 -M "?" 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus3.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 2 -M "?" 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus3.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 2 -M "?" -p xx_ 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus3.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -H 2 -M "?" -p xx_ 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus4.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus4.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus5.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus5.fa --haplotype LA 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus5.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus5.fa --haplotype LA 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus6.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus6.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus6.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus6.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 2 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 2 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 4 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 4 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 2pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 2pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 4pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 4pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 1 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 1 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 3 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 3 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 1pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 1pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 3pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus7.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus7.fa -H 3pIu 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -i 'ALT!=""' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -i 'ALT!=""' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -e 'MinDP>15' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -e 'MinDP>15' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -e 'MinDP<15' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus8.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -a . -e 'MinDP<15' 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.9.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.1.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.9.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.1.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.9.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.2.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.9.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.2.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.10.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.1.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.10.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.1.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.10.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.2.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.10.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.9.2.fa -H A 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.11.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.11.fa -s smpl 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.11.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.11.fa -s smpl 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.11.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.11.fa -s smpl -a N 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.11.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.11.fa -s smpl -a N 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.12.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.12.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.12.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.12.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.13.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.13.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.13.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.13.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.14.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.14.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.14.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.14.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.12.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.12.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.12.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.12.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.15.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.15.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.16.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -I 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.16.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -s - -I 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.16.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H I 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.16.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.fa -H I 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.17.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -s - -M N -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.17.bed 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.17.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus2.fa -s - -M N -m /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.17.bed 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.18.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.18.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.18.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.18.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.19.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.19.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.19.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.19.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa -s - 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa -M . -s b 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa -M . -s b 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa -M . -s a 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.20.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.20.fa -M . -s a 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.21.vcf.gz -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.21.fa 317s .. ok 317s 317s test_vcf_consensus: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools consensus /tmp/Luz3rC8Wiv/consensus.21.bcf -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/consensus.21.fa 317s .. ok 317s 317s test_mpileup: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 317s .. ok 317s 317s test_mpileup: 317s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -b /tmp/Luz3rC8Wiv/mpileup.bam.list --no-version | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob -b /tmp/Luz3rC8Wiv/mpileup.bam.urllist | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -b /tmp/Luz3rC8Wiv/mpileup.cram.list --no-version | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob -b /tmp/Luz3rC8Wiv/mpileup.cram.urllist | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 318s .. ok 318s 318s test_mpileup: 318s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 319s .. ok 319s 319s test_mpileup: 319s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 320s .. ok 320s 320s test_mpileup: 320s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/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 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/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 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/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 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/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 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 321s .. ok 321s 321s test_mpileup: 321s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 322s .. ok 322s 322s test_mpileup: 322s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 323s .. ok 323s 323s test_mpileup: 323s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.9.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.9.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.9.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.9.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.9.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.9.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.10.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.10.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 324s .. ok 324s 324s test_mpileup: 324s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.10.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.10.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.10.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.10.samples -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference 325s .. ok 325s 325s test_mpileup: 325s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 326s .. ok 326s 326s test_mpileup: 326s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference 326s .. ok 326s 326s test_mpileup: 326s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 326s .. ok 326s 326s test_mpileup: 326s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference 326s .. ok 326s 326s test_mpileup: 326s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 326s .. ok 326s 326s test_mpileup: 326s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference 326s .. ok 326s 326s test_mpileup: 326s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 327s .. ok 327s 327s test_mpileup: 327s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference 328s .. ok 328s 328s test_mpileup: 328s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 328s .. ok 328s 328s test_mpileup: 328s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference 328s .. ok 328s 328s test_mpileup: 328s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 328s .. ok 328s 328s test_mpileup: 328s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference 328s .. ok 328s 328s test_mpileup: 328s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 328s .. ok 328s 328s test_mpileup: 328s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference 329s .. ok 329s 329s test_mpileup: 329s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -G /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mplp.11.rgs -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.1.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 330s .. ok 330s 330s test_mpileup: 330s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 331s .. ok 331s 331s test_mpileup: 331s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference 332s .. ok 332s 332s test_mpileup: 332s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.cram | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference 333s .. ok 333s 333s test_mpileup: 333s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_mpileup: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.1.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_mpileup: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.1.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.1.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_mpileup: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.2.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_mpileup: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.2.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.2.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_mpileup: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.3.fa /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.3.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_mpileup: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.3.fa -Ob /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.3.1.bam /tmp/autopkgtest.ig2rlO/build.E6f/src/test/mpileup/annot-NMBZ.3.2.bam | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools view | grep -v ^##bcftools | grep -v ^##reference 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.gff3 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.chr.gff3 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.2.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.2.gff --ncsq 64 /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 334s .. ok 334s 334s test_csq: 334s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 335s .. ok 335s 335s test_csq: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 335s .. ok 335s 335s test_csq: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.nchr.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq.ychr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000227471/ENST00000227471.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000227471/ENST00000227471.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000382647/ENST00000382647.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000382647/ENST00000382647.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000357367/ENST00000357367.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000357367/ENST00000357367.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000357367/stop-retained.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000409523/ENST00000409523.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000409523/ENST00000409523.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000409523/long-overlapping-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000303039/ENST00000303039.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000303039/ENST00000303039.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000303039/not-a-stop.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000303039/ENST00000303039.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000303039/ENST00000303039.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000303039/not-a-stop.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000413103/ENST00000413103.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000413103/ENST00000413103.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000413103/long-deletion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000536784/ENST00000536784.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000536784/ENST00000536784.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000536784/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000536784/ENST00000536784.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000536784/ENST00000536784.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000536784/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000422159 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000400151/ENST00000400151.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000400151/ENST00000400151.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000400151/long-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000373833/ENST00000373833.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000373833/ENST00000373833.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000373833/boundary-insertion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000373833/ENST00000373833.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000373833/ENST00000373833.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000373833/boundary-insertion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420670/ENST00000420670.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420670/ENST00000420670.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420670/segfault.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420670/ENST00000420670.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420670/ENST00000420670.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420670/start-stop-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000448695/ENST00000448695.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000448695/ENST00000448695.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000269081/ENST00000269081.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000269081/ENST00000269081.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000360372/ENST00000360372.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000360372/ENST00000360372.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000360372/mnp.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSG00000173376/ENSG00000173376.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSG00000173376/ENSG00000173376.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSG00000173376/synon.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249/ENST00000318249.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249/ENST00000318249.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249/start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249/ENST00000318249.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249/ENST00000318249.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249/start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000295641/ENST00000295641.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000295641/ENST00000295641.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000295641/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000295641/ENST00000295641.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000295641/ENST00000295641.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000295641/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000580206 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000479739/ENST00000479739.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000479739/ENST00000479739.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000479739/short-cds-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000479739/ENST00000479739.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000479739/ENST00000479739.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000479739/short-cds-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0002/EDUMMY0002.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0002/EDUMMY0002.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0002/boundaries.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000528237/ENST00000528237.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000528237/ENST00000528237.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000545279/ENST00000545279.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000545279/ENST00000545279.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000545279/splice-region-insert.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000543077/ENST00000543077.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000543077/ENST00000543077.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000543077/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000543077/ENST00000543077.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000543077/ENST00000543077.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000543077/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000294661/ENST00000294661.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000294661/ENST00000294661.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000294661/non-coding-boundary.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000294661/ENST00000294661.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000294661/ENST00000294661.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000294661/non-coding-boundary.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000593942/ENST00000593942.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000593942/ENST00000593942.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000593942/last-codon-deletion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000381157/ENST00000381157.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000381157/ENST00000381157.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000381157/haploid-diploid.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420190/ENST00000420190.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420190/ENST00000420190.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000420190/abort-in-csq-push.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/snps.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/snps.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/insert3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000423372/insert3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000573314/ENST00000573314.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000573314/ENST00000573314.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000573314/ENST00000573314.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000573314/ENST00000573314.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249.2/ENST00000318249.2.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000271583/ENST00000271583.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000271583/ENST00000271583.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000271583/splice-acceptor.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000436063/ENST00000436063.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000436063/ENST00000436063.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000436063/insert-before-utr.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000368801/ENST00000368801.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000368801/ENST00000368801.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000368801/compound-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000557788/ENST00000557788.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000557788/ENST00000557788.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000557788/long-overlap-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000624631/ENST00000624631.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000624631/ENST00000624631.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000624631/ambiguous.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000256452/ENST00000256452.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000256452/ENST00000256452.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000256452/intron.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSMUST00000133836 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000301246/ENST00000301246.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000301246/ENST00000301246.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000301246/15bp-insert.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 335s .. ok 335s 335s test_csq_real: 335s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000379416 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 335s .. ok 335s 335s test_csq_real: 335s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0001/EDUMMY0001.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0001/EDUMMY0001.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0001/starts-with-1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0001/EDUMMY0001.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0001/EDUMMY0001.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0001/starts-with-1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520868/ENST00000520868.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520868/ENST00000520868.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520868/long-deletion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EMN908947 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EMN908947 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000375992/ENST00000375992.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000375992/ENST00000375992.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520795/ENST00000520795.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520795/ENST00000520795.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520795/long-inside-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520795/ENST00000520795.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520795/ENST00000520795.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000520795/long-inside-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000519442/ENST00000519442.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000519442/ENST00000519442.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000519442/synon-splice-region-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000285021/ENST00000285021.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000285021/ENST00000285021.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000410009 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000410009 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000410009 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000410009/ENST00000410009.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000410009/ENST00000410009.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000410009/frameshift.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s cd /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000000000 && /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000378322/ENST00000378322.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000378322/ENST00000378322.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000378322/end-overlap-tscript.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000378322/ENST00000378322.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000378322/ENST00000378322.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000378322/end-overlap-tscript.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000518414/ENST00000518414.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000518414/ENST00000518414.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/frame3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/frame3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/frame2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/frame2.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/not-a-start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/frame1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000341065/frame1.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000230048/ENST00000230048.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000230048/ENST00000230048.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000230048/start-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0003/EDUMMY0003.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0003/EDUMMY0003.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/EDUMMY0003/long-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000329454/ENST00000329454.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000329454/ENST00000329454.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000329454/boundary-deletion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000329454/ENST00000329454.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000329454/ENST00000329454.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000329454/boundary-deletion.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000390520/ENST00000390520.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000390520/ENST00000390520.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000390520/deletion-overlap.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000263103-INS/insertions.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000218032/start-lost-del.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000368801.2/ENST00000368801.2.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000368801.2/start-lost.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000571540/ENST00000571540.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000571540/ENST00000571540.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000571540/nmd.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000542803/ENST00000542803.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000542803/ENST00000542803.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000542803/splice-region.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_csq_real: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools csq -l -f /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000542803/ENST00000542803.fa -g /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000542803/ENST00000542803.gff /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/ENST00000542803/splice-region.vcf | /tmp/autopkgtest.ig2rlO/build.E6f/src/test/csq/sort-csq | /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -Or -G30 --AF-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.tab.gz| grep -v ^# 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -Or -G30 --AF-file /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.tab.gz --ignore-homref| grep -v ^# 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# 336s .. ok 336s 336s test_roh: 336s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools roh /tmp/autopkgtest.ig2rlO/build.E6f/src/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# 336s .. ok 336s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u GT,GT /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u GT,PL /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u PL,GT /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u PL,PL /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -p s1,s1 /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 /tmp/Luz3rC8Wiv/gtcheck.2.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/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/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gtcheck.3.pairs /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u PL /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 --n-matches 4 /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -p B,C,B,D /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u GT,GT -H /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u GT,PL -H /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u PL,GT -H /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -u PL,PL -H /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/Luz3rC8Wiv/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.ig2rlO/build.E6f/src/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/Luz3rC8Wiv/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -u GT -e 30 /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -u GT -e 300 /tmp/Luz3rC8Wiv/gtcheck.1.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -u PL -e 30 /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck /tmp/Luz3rC8Wiv/gtcheck.ntop.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck --n-matches 2 /tmp/Luz3rC8Wiv/gtcheck.ntop.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck /tmp/Luz3rC8Wiv/gtcheck.5.vcf.gz -g /tmp/Luz3rC8Wiv/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -p A,B,B,C /tmp/Luz3rC8Wiv/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s test_gtcheck: 337s /tmp/autopkgtest.ig2rlO/build.E6f/src/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/Luz3rC8Wiv/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO 337s .. ok 337s 337s 337s Number of tests: 337s total .. 1662 337s passed .. 1662 337s failed .. 0 337s 337s mv: cannot stat 'bcftools.orig': No such file or directory 337s autopkgtest [19:44:07]: test command1: -----------------------] 338s autopkgtest [19:44:08]: test command1: - - - - - - - - - - results - - - - - - - - - - 338s command1 PASS 338s autopkgtest [19:44:08]: @@@@@@@@@@@@@@@@@@@@ summary 338s command1 PASS 351s Creating nova instance adt-noble-ppc64el-bcftools-20240325-193830-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...