0s autopkgtest [02:36:55]: starting date and time: 2024-03-27 02:36:55+0000
  0s autopkgtest [02:36:55]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [02:36:55]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vd0i0mhw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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@bos03-arm64-15.secgroup --name adt-noble-arm64-bcftools-20240327-023654-juju-7f2275-prod-proposed-migration-environment-3-a62d65d0-7fa3-46e9-bddb-fa0a37b43ee6 --image adt/ubuntu-noble-arm64-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/
 67s autopkgtest [02:38:02]: testbed dpkg architecture: arm64
 67s autopkgtest [02:38:02]: testbed apt version: 2.7.12
 67s autopkgtest [02:38:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 68s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 68s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B]
 68s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.4 kB]
 68s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
 68s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB]
 69s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [717 kB]
 69s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 69s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [43.0 kB]
 69s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 69s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4303 kB]
 69s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 69s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB]
 69s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 71s Fetched 9808 kB in 2s (5231 kB/s)
 71s Reading package lists...
 75s Reading package lists...
 75s Building dependency tree...
 75s Reading state information...
 76s Calculating upgrade...
 77s The following packages will be REMOVED:
 77s   libssl3
 77s The following NEW packages will be installed:
 77s   libssl3t64
 77s The following packages have been kept back:
 77s   curl
 77s The following packages will be upgraded:
 77s   openssl
 77s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
 77s Need to get 2777 kB of archives.
 77s After this operation, 139 kB of additional disk space will be used.
 77s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
 78s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
 79s Fetched 2777 kB in 1s (3886 kB/s)
 79s (Reading database ... 
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(Reading database ... 74816 files and directories currently installed.)
 79s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
 79s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
 79s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
 79s  wget depends on libssl3 (>= 3.0.0).
 79s  u-boot-tools depends on libssl3 (>= 3.0.0).
 79s  tnftp depends on libssl3 (>= 3.0.0).
 79s  tcpdump depends on libssl3 (>= 3.0.0).
 79s  systemd-resolved depends on libssl3 (>= 3.0.0).
 79s  systemd depends on libssl3 (>= 3.0.0).
 79s  sudo depends on libssl3 (>= 3.0.0).
 79s  sbsigntool depends on libssl3 (>= 3.0.0).
 79s  rsync depends on libssl3 (>= 3.0.0).
 79s  python3-cryptography depends on libssl3 (>= 3.0.0).
 79s  openssh-server depends on libssl3 (>= 3.0.10).
 79s  openssh-client depends on libssl3 (>= 3.0.10).
 79s  mtd-utils depends on libssl3 (>= 3.0.0).
 79s  mokutil depends on libssl3 (>= 3.0.0).
 79s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
 79s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
 79s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
 79s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
 79s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
 79s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
 79s  libnvme1 depends on libssl3 (>= 3.0.0).
 79s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
 79s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
 79s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
 79s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
 79s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
 79s  kmod depends on libssl3 (>= 3.0.0).
 79s  dhcpcd-base depends on libssl3 (>= 3.0.0).
 79s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
 79s 
 79s (Reading database ... 
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(Reading database ... 74816 files and directories currently installed.)
 79s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
 79s Selecting previously unselected package libssl3t64:arm64.
 79s (Reading database ... 
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(Reading database ... 74805 files and directories currently installed.)
 79s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
 79s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
 79s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
 79s Setting up openssl (3.0.13-0ubuntu2) ...
 79s Processing triggers for man-db (2.12.0-3) ...
 80s Processing triggers for libc-bin (2.39-0ubuntu6) ...
 80s Reading package lists...
 81s Building dependency tree...
 81s Reading state information...
 81s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 82s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 82s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 82s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 82s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
 84s Reading package lists...
 84s Reading package lists...
 84s Building dependency tree...
 84s Reading state information...
 85s Calculating upgrade...
 85s The following packages have been kept back:
 85s   curl
 85s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 85s Reading package lists...
 86s Building dependency tree...
 86s Reading state information...
 86s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 89s autopkgtest [02:38:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
 89s autopkgtest [02:38:24]: @@@@@@@@@@@@@@@@@@@@ apt-source bcftools
 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe bcftools 1.19-1build1 (dsc) [2260 B]
 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe bcftools 1.19-1build1 (tar) [3540 kB]
 92s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe bcftools 1.19-1build1 (diff) [11.2 kB]
 92s gpgv: Signature made Fri Mar 22 15:49:59 2024 UTC
 92s gpgv:                using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71
 92s gpgv:                issuer "juliank@ubuntu.com"
 92s gpgv: Can't check signature: No public key
 92s dpkg-source: warning: cannot verify inline signature for ./bcftools_1.19-1build1.dsc: no acceptable signature found
 92s autopkgtest [02:38:27]: testing package bcftools version 1.19-1build1
 92s autopkgtest [02:38:27]: build not needed
 94s autopkgtest [02:38:29]: test command1: preparing testbed
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 96s Starting pkgProblemResolver with broken count: 0
 96s Starting 2 pkgProblemResolver with broken count: 0
 96s Done
 96s The following additional packages will be installed:
 96s   bcftools curl libcurl3t64-gnutls libcurl4t64 libdeflate0 libgnutls30t64
 96s   libhogweed6t64 libhts3t64 libhtscodecs2 libnettle8t64 libpsl5t64 tabix
 96s Suggested packages:
 96s   python3-numpy python3-matplotlib texlive-latex-recommended gnutls-bin
 96s The following packages will be REMOVED:
 96s   libcurl3-gnutls libcurl4 libgnutls30 libhogweed6 libnettle8 libpsl5
 96s The following NEW packages will be installed:
 96s   autopkgtest-satdep bcftools libcurl3t64-gnutls libcurl4t64 libdeflate0
 96s   libgnutls30t64 libhogweed6t64 libhts3t64 libhtscodecs2 libnettle8t64
 96s   libpsl5t64 tabix
 96s The following packages will be upgraded:
 96s   curl
 96s 1 upgraded, 12 newly installed, 6 to remove and 0 not upgraded.
 96s Need to get 4198 kB/4199 kB of archives.
 96s After this operation, 8636 kB of additional disk space will be used.
 96s Get:1 /tmp/autopkgtest.RAARSc/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B]
 97s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2 [192 kB]
 97s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2 [199 kB]
 97s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu2 [1042 kB]
 97s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu8 [332 kB]
 97s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu8 [222 kB]
 97s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB]
 97s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl3t64-gnutls arm64 8.5.0-2ubuntu8 [327 kB]
 97s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
 97s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
 97s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3t64 arm64 1.19+ds-1.1build2 [429 kB]
 97s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 bcftools arm64 1.19-1build1 [762 kB]
 97s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 tabix arm64 1.19+ds-1.1build2 [515 kB]
 98s Fetched 4198 kB in 1s (4862 kB/s)
 98s dpkg: libhogweed6:arm64: dependency problems, but removing anyway as you requested:
 98s  librtmp1:arm64 depends on libhogweed6.
 98s  libjcat1:arm64 depends on libhogweed6.
 98s  libgnutls30:arm64 depends on libhogweed6 (>= 3.6).
 98s 
 98s (Reading database ... 
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(Reading database ... 74818 files and directories currently installed.)
 98s Removing libhogweed6:arm64 (3.9.1-2) ...
 98s dpkg: libnettle8:arm64: dependency problems, but removing anyway as you requested:
 98s  librtmp1:arm64 depends on libnettle8.
 98s  libgnutls30:arm64 depends on libnettle8 (>= 3.9~).
 98s  libcurl3-gnutls:arm64 depends on libnettle8.
 98s  libarchive13:arm64 depends on libnettle8.
 98s 
 98s Removing libnettle8:arm64 (3.9.1-2) ...
 98s Selecting previously unselected package libnettle8t64:arm64.
 98s (Reading database ... 
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(Reading database ... 74806 files and directories currently installed.)
 98s Preparing to unpack .../libnettle8t64_3.9.1-2.2_arm64.deb ...
 98s Unpacking libnettle8t64:arm64 (3.9.1-2.2) ...
 98s Selecting previously unselected package libhogweed6t64:arm64.
 98s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_arm64.deb ...
 98s Unpacking libhogweed6t64:arm64 (3.9.1-2.2) ...
 98s dpkg: libgnutls30:arm64: dependency problems, but removing anyway as you requested:
 98s  u-boot-tools depends on libgnutls30 (>= 3.7.3).
 98s  librtmp1:arm64 depends on libgnutls30 (>= 3.7.2).
 98s  libldap2:arm64 depends on libgnutls30 (>= 3.8.2).
 98s  libjcat1:arm64 depends on libgnutls30 (>= 3.7.3).
 98s  libcurl3-gnutls:arm64 depends on libgnutls30 (>= 3.8.2).
 98s  fwupd depends on libgnutls30 (>= 3.7.3).
 98s  dirmngr depends on libgnutls30 (>= 3.8.1).
 98s  apt depends on libgnutls30 (>= 3.8.1).
 98s 
 98s (Reading database ... 
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(Reading database ... 74820 files and directories currently installed.)
 98s Removing libgnutls30:arm64 (3.8.3-1ubuntu1) ...
 98s Selecting previously unselected package libgnutls30t64:arm64.
 98s (Reading database ... 
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(Reading database ... 74811 files and directories currently installed.)
 98s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_arm64.deb ...
 98s Unpacking libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ...
 98s dpkg: libcurl4:arm64: dependency problems, but removing anyway as you requested:
 98s  curl depends on libcurl4 (= 8.5.0-2ubuntu2).
 98s 
 98s (Reading database ... 
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(Reading database ... 74839 files and directories currently installed.)
 98s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ...
 98s Selecting previously unselected package libcurl4t64:arm64.
 98s (Reading database ... 
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(Reading database ... 74834 files and directories currently installed.)
 98s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu8_arm64.deb ...
 98s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu8) ...
 99s Preparing to unpack .../curl_8.5.0-2ubuntu8_arm64.deb ...
 99s Unpacking curl (8.5.0-2ubuntu8) over (8.5.0-2ubuntu2) ...
 99s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested:
 99s  wget depends on libpsl5 (>= 0.16.0).
 99s  libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0).
 99s 
 99s (Reading database ... 
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(Reading database ... 74840 files and directories currently installed.)
 99s Removing libpsl5:arm64 (0.21.2-1build1) ...
 99s Selecting previously unselected package libpsl5t64:arm64.
 99s (Reading database ... 
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(Reading database ... 74835 files and directories currently installed.)
 99s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ...
 99s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ...
 99s dpkg: libcurl3-gnutls:arm64: dependency problems, but removing anyway as you requested:
 99s  libfwupd2:arm64 depends on libcurl3-gnutls (>= 7.63.0).
 99s  fwupd depends on libcurl3-gnutls (>= 7.63.0).
 99s 
 99s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 74841 files and directories currently installed.)
 99s Removing libcurl3-gnutls:arm64 (8.5.0-2ubuntu2) ...
 99s Selecting previously unselected package libcurl3t64-gnutls:arm64.
 99s (Reading database ... 
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(Reading database ... 74834 files and directories currently installed.)
 99s Preparing to unpack .../0-libcurl3t64-gnutls_8.5.0-2ubuntu8_arm64.deb ...
 99s Unpacking libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu8) ...
 99s Selecting previously unselected package libdeflate0:arm64.
 99s Preparing to unpack .../1-libdeflate0_1.19-1_arm64.deb ...
 99s Unpacking libdeflate0:arm64 (1.19-1) ...
 99s Selecting previously unselected package libhtscodecs2:arm64.
 99s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_arm64.deb ...
 99s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
 99s Selecting previously unselected package libhts3t64:arm64.
 99s Preparing to unpack .../3-libhts3t64_1.19+ds-1.1build2_arm64.deb ...
 99s Unpacking libhts3t64:arm64 (1.19+ds-1.1build2) ...
 99s Selecting previously unselected package bcftools.
 99s Preparing to unpack .../4-bcftools_1.19-1build1_arm64.deb ...
 99s Unpacking bcftools (1.19-1build1) ...
 99s Selecting previously unselected package tabix.
 99s Preparing to unpack .../5-tabix_1.19+ds-1.1build2_arm64.deb ...
 99s Unpacking tabix (1.19+ds-1.1build2) ...
 99s Selecting previously unselected package autopkgtest-satdep.
 99s Preparing to unpack .../6-1-autopkgtest-satdep.deb ...
 99s Unpacking autopkgtest-satdep (0) ...
 99s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
 99s Setting up libpsl5t64:arm64 (0.21.2-1.1) ...
 99s Setting up libdeflate0:arm64 (1.19-1) ...
 99s Setting up libnettle8t64:arm64 (3.9.1-2.2) ...
 99s Setting up libhogweed6t64:arm64 (3.9.1-2.2) ...
 99s Setting up tabix (1.19+ds-1.1build2) ...
 99s Setting up libgnutls30t64:arm64 (3.8.3-1.1ubuntu2) ...
 99s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu8) ...
 99s Setting up libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu8) ...
 99s Setting up libhts3t64:arm64 (1.19+ds-1.1build2) ...
 99s Setting up curl (8.5.0-2ubuntu8) ...
 99s Setting up bcftools (1.19-1build1) ...
 99s Setting up autopkgtest-satdep (0) ...
 99s Processing triggers for man-db (2.12.0-3) ...
 99s Processing triggers for libc-bin (2.39-0ubuntu6) ...
103s (Reading database ... 74931 files and directories currently installed.)
103s Removing autopkgtest-satdep (0) ...
104s autopkgtest [02:38:39]: 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
104s autopkgtest [02:38:39]: test command1: [-----------------------
104s mv: cannot stat 'bcftools': No such file or directory
104s ./test/test.pl: module IO::Pty not found; skipping usage tests
104s test_usage:
104s 	bcftools
104s test_tabix:
104s 	/usr/bin/tabix /tmp/N9wvQi6tqJ/merge.a.vcf.gz 2:3199812-3199812
104s .. ok
104s 
104s test_tabix:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/merge.a.bcf 2:3199812-3199812
104s .. ok
104s 
104s test_tabix:
104s 	/usr/bin/tabix /tmp/N9wvQi6tqJ/merge.a.vcf.gz 1:3000151-3000151
104s .. ok
104s 
104s test_tabix:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/merge.a.bcf 1:3000151-3000151
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.bcf chr20:1-2147483647
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.bcf chr20:1-2147483647
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.bcf chr20:1-2147483647
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.vcf.gz chr20
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.bcf chr20
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.bcf chr20
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.vcf.gz chr20
104s .. ok
104s 
104s test_index:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H /tmp/N9wvQi6tqJ/large_chrom_csi_limit.bcf chr20
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -s /tmp/N9wvQi6tqJ/idx.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -s /tmp/N9wvQi6tqJ/idx.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -s /tmp/N9wvQi6tqJ/idx.bcf
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/idx.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/idx.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/idx.vcf.gz.csi
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/idx.bcf
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/idx.bcf.csi
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -s /tmp/N9wvQi6tqJ/empty.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -s /tmp/N9wvQi6tqJ/empty.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -s /tmp/N9wvQi6tqJ/empty.bcf
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/empty.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/empty.vcf.gz
104s .. ok
104s 
104s test_vcf_idxstats:
104s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/empty.vcf.gz.csi
105s .. ok
105s 
105s test_vcf_idxstats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/empty.bcf
105s .. ok
105s 
105s test_vcf_idxstats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools index -n /tmp/N9wvQi6tqJ/empty.bcf.csi
105s .. ok
105s 
105s test_vcf_check:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s - /tmp/N9wvQi6tqJ/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_check:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_check_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/misc/plot-vcfstats -m /tmp/N9wvQi6tqJ/check.1.chk /tmp/N9wvQi6tqJ/check.2.chk /tmp/N9wvQi6tqJ/check.3.chk /tmp/N9wvQi6tqJ/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_stats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s -  /tmp/N9wvQi6tqJ/stats.a.vcf.gz /tmp/N9wvQi6tqJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_stats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s B  /tmp/N9wvQi6tqJ/stats.a.vcf.gz /tmp/N9wvQi6tqJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_stats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s -  /tmp/N9wvQi6tqJ/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_stats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s - -i 'type="snp"'  /tmp/N9wvQi6tqJ/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_stats:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools stats -s -  /tmp/N9wvQi6tqJ/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID	'
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -n =2 /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -n =2 /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -n =2 -c both /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -n =2 -c both /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -n =2 -c any /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -n =2 -c any /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -C -c any /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -C -c any /tmp/N9wvQi6tqJ/isec.a.vcf.gz /tmp/N9wvQi6tqJ/isec.b.vcf.gz
105s .. ok
105s 
105s test_vcf_isec2:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec --no-version   -T /tmp/N9wvQi6tqJ/isec.tab.gz /tmp/N9wvQi6tqJ/isec.a.vcf.gz
105s .. ok
105s 
105s test_vcf_isec2:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob  -T /tmp/N9wvQi6tqJ/isec.tab.gz /tmp/N9wvQi6tqJ/isec.a.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/N9wvQi6tqJ/isec-miss.1.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/N9wvQi6tqJ/isec-miss.1.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/isec-miss.1.regs.txt -n +1 /tmp/N9wvQi6tqJ/isec-miss.1.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/isec-miss.1.regs.txt -n +1 /tmp/N9wvQi6tqJ/isec-miss.1.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.1.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/N9wvQi6tqJ/isec-miss.2.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/N9wvQi6tqJ/isec-miss.2.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/isec-miss.1.regs.txt -n +1 /tmp/N9wvQi6tqJ/isec-miss.2.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.3.vcf.gz
105s .. ok
105s 
105s test_vcf_isec:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools isec -Ob -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/isec-miss.1.regs.txt -n +1 /tmp/N9wvQi6tqJ/isec-miss.2.1.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.2.vcf.gz /tmp/N9wvQi6tqJ/isec-miss.2.3.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -i AF:join /tmp/N9wvQi6tqJ/merge.join.a.vcf.gz /tmp/N9wvQi6tqJ/merge.join.b.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -i AF:join /tmp/N9wvQi6tqJ/merge.join.a.vcf.gz /tmp/N9wvQi6tqJ/merge.join.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -i AF:join /tmp/N9wvQi6tqJ/merge.join.a.bcf /tmp/N9wvQi6tqJ/merge.join.b.bcf
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -i AF:join /tmp/N9wvQi6tqJ/merge.join.a.bcf /tmp/N9wvQi6tqJ/merge.join.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 1 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 1 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 2 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 2 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 3 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 3 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 4 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 4 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 5 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/N9wvQi6tqJ/merge.LPL.a.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.b.vcf.gz /tmp/N9wvQi6tqJ/merge.LPL.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
105s .. ok
105s 
105s test_vcf_merge:
105s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -L 5 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/N9wvQi6tqJ/merge.LPL.a.bcf /tmp/N9wvQi6tqJ/merge.LPL.b.bcf /tmp/N9wvQi6tqJ/merge.LPL.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples /tmp/N9wvQi6tqJ/merge.a.vcf.gz /tmp/N9wvQi6tqJ/merge.b.vcf.gz /tmp/N9wvQi6tqJ/merge.c.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples /tmp/N9wvQi6tqJ/merge.a.vcf.gz /tmp/N9wvQi6tqJ/merge.b.vcf.gz /tmp/N9wvQi6tqJ/merge.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples /tmp/N9wvQi6tqJ/merge.a.bcf /tmp/N9wvQi6tqJ/merge.b.bcf /tmp/N9wvQi6tqJ/merge.c.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples /tmp/N9wvQi6tqJ/merge.a.bcf /tmp/N9wvQi6tqJ/merge.b.bcf /tmp/N9wvQi6tqJ/merge.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -Fx /tmp/N9wvQi6tqJ/merge.a.vcf.gz /tmp/N9wvQi6tqJ/merge.b.vcf.gz /tmp/N9wvQi6tqJ/merge.c.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -Fx /tmp/N9wvQi6tqJ/merge.a.vcf.gz /tmp/N9wvQi6tqJ/merge.b.vcf.gz /tmp/N9wvQi6tqJ/merge.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -Fx /tmp/N9wvQi6tqJ/merge.a.bcf /tmp/N9wvQi6tqJ/merge.b.bcf /tmp/N9wvQi6tqJ/merge.c.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -Fx /tmp/N9wvQi6tqJ/merge.a.bcf /tmp/N9wvQi6tqJ/merge.b.bcf /tmp/N9wvQi6tqJ/merge.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -0 /tmp/N9wvQi6tqJ/merge.a.vcf.gz /tmp/N9wvQi6tqJ/merge.b.vcf.gz /tmp/N9wvQi6tqJ/merge.c.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -0 /tmp/N9wvQi6tqJ/merge.a.vcf.gz /tmp/N9wvQi6tqJ/merge.b.vcf.gz /tmp/N9wvQi6tqJ/merge.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -0 /tmp/N9wvQi6tqJ/merge.a.bcf /tmp/N9wvQi6tqJ/merge.b.bcf /tmp/N9wvQi6tqJ/merge.c.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -0 /tmp/N9wvQi6tqJ/merge.a.bcf /tmp/N9wvQi6tqJ/merge.b.bcf /tmp/N9wvQi6tqJ/merge.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m none /tmp/N9wvQi6tqJ/merge.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.2.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m none /tmp/N9wvQi6tqJ/merge.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.2.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m none /tmp/N9wvQi6tqJ/merge.2.a.bcf /tmp/N9wvQi6tqJ/merge.2.b.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m none /tmp/N9wvQi6tqJ/merge.2.a.bcf /tmp/N9wvQi6tqJ/merge.2.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m both /tmp/N9wvQi6tqJ/merge.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.2.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m both /tmp/N9wvQi6tqJ/merge.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.2.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m both /tmp/N9wvQi6tqJ/merge.2.a.bcf /tmp/N9wvQi6tqJ/merge.2.b.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m both /tmp/N9wvQi6tqJ/merge.2.a.bcf /tmp/N9wvQi6tqJ/merge.2.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m all /tmp/N9wvQi6tqJ/merge.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.2.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m all /tmp/N9wvQi6tqJ/merge.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.2.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m all /tmp/N9wvQi6tqJ/merge.2.a.bcf /tmp/N9wvQi6tqJ/merge.2.b.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m all /tmp/N9wvQi6tqJ/merge.2.a.bcf /tmp/N9wvQi6tqJ/merge.2.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/N9wvQi6tqJ/merge.3.a.vcf.gz /tmp/N9wvQi6tqJ/merge.3.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/N9wvQi6tqJ/merge.3.a.vcf.gz /tmp/N9wvQi6tqJ/merge.3.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/N9wvQi6tqJ/merge.3.a.bcf /tmp/N9wvQi6tqJ/merge.3.b.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/N9wvQi6tqJ/merge.3.a.bcf /tmp/N9wvQi6tqJ/merge.3.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m id /tmp/N9wvQi6tqJ/merge.4.a.vcf.gz /tmp/N9wvQi6tqJ/merge.4.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m id /tmp/N9wvQi6tqJ/merge.4.a.vcf.gz /tmp/N9wvQi6tqJ/merge.4.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples -m id /tmp/N9wvQi6tqJ/merge.4.a.bcf /tmp/N9wvQi6tqJ/merge.4.b.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples -m id /tmp/N9wvQi6tqJ/merge.4.a.bcf /tmp/N9wvQi6tqJ/merge.4.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/gvcf.merge.1.vcf.gz /tmp/N9wvQi6tqJ/gvcf.merge.2.vcf.gz /tmp/N9wvQi6tqJ/gvcf.merge.3.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/gvcf.merge.1.vcf.gz /tmp/N9wvQi6tqJ/gvcf.merge.2.vcf.gz /tmp/N9wvQi6tqJ/gvcf.merge.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/gvcf.merge.1.bcf /tmp/N9wvQi6tqJ/gvcf.merge.2.bcf /tmp/N9wvQi6tqJ/gvcf.merge.3.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/gvcf.merge.1.bcf /tmp/N9wvQi6tqJ/gvcf.merge.2.bcf /tmp/N9wvQi6tqJ/gvcf.merge.3.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.c.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - -m both,* /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.c.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - -m both,** /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.c.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - -i SRC:join /tmp/N9wvQi6tqJ/merge.gvcf.3.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.3.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/N9wvQi6tqJ/merge.gvcf.3.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.3.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.4.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.4.b.vcf.gz
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.4.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.4.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.4.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.4.b.bcf
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.4.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.4.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
106s .. ok
106s 
106s test_vcf_merge:
106s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.5.a.vcf.gz /tmp/N9wvQi6tqJ/merge.5.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.5.a.vcf.gz /tmp/N9wvQi6tqJ/merge.5.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.5.a.bcf /tmp/N9wvQi6tqJ/merge.5.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.5.a.bcf /tmp/N9wvQi6tqJ/merge.5.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.6.a.vcf.gz /tmp/N9wvQi6tqJ/merge.6.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.6.a.vcf.gz /tmp/N9wvQi6tqJ/merge.6.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.6.a.bcf /tmp/N9wvQi6tqJ/merge.6.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.6.a.bcf /tmp/N9wvQi6tqJ/merge.6.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.7.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.7.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.7.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.7.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.7.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.7.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.7.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.7.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.8.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.8.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.8.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.8.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.8.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.8.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.8.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.8.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples /tmp/N9wvQi6tqJ/merge.7.a.vcf.gz /tmp/N9wvQi6tqJ/merge.7.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples /tmp/N9wvQi6tqJ/merge.7.a.vcf.gz /tmp/N9wvQi6tqJ/merge.7.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --force-samples /tmp/N9wvQi6tqJ/merge.7.a.bcf /tmp/N9wvQi6tqJ/merge.7.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --force-samples /tmp/N9wvQi6tqJ/merge.7.a.bcf /tmp/N9wvQi6tqJ/merge.7.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9e.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9e.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9e.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9e.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9e.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9c.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9d.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.9e.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9e.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa -r 22:21-23 /tmp/N9wvQi6tqJ/merge.gvcf.9a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9c.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9d.bcf /tmp/N9wvQi6tqJ/merge.gvcf.9e.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz
107s .. ok
107s 
107s test_vcf_merge:
107s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.gvcf.10.fa -m none /tmp/N9wvQi6tqJ/merge.gvcf.10.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.noidx.a.vcf.gz /tmp/N9wvQi6tqJ/merge.noidx.b.vcf.gz /tmp/N9wvQi6tqJ/merge.noidx.c.vcf.gz
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.noidx.a.vcf.gz /tmp/N9wvQi6tqJ/merge.noidx.b.vcf.gz /tmp/N9wvQi6tqJ/merge.noidx.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.noidx.a.bcf /tmp/N9wvQi6tqJ/merge.noidx.b.bcf /tmp/N9wvQi6tqJ/merge.noidx.c.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.noidx.a.bcf /tmp/N9wvQi6tqJ/merge.noidx.b.bcf /tmp/N9wvQi6tqJ/merge.noidx.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --no-index /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.noidx.a.vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.noidx.b.vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.noidx.c.vcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --no-index /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.noidx.a.vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.noidx.b.vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/merge.noidx.c.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --no-index /tmp/N9wvQi6tqJ/merge.noidx.a.bcf /tmp/N9wvQi6tqJ/merge.noidx.b.bcf /tmp/N9wvQi6tqJ/merge.noidx.c.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --no-index /tmp/N9wvQi6tqJ/merge.noidx.a.bcf /tmp/N9wvQi6tqJ/merge.noidx.b.bcf /tmp/N9wvQi6tqJ/merge.noidx.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.8.a.vcf.gz /tmp/N9wvQi6tqJ/merge.8.b.vcf.gz
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.8.a.vcf.gz /tmp/N9wvQi6tqJ/merge.8.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.8.a.bcf /tmp/N9wvQi6tqJ/merge.8.b.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.8.a.bcf /tmp/N9wvQi6tqJ/merge.8.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.8.a.vcf.gz /tmp/N9wvQi6tqJ/merge.8.b.vcf.gz
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.8.a.vcf.gz /tmp/N9wvQi6tqJ/merge.8.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.8.a.bcf /tmp/N9wvQi6tqJ/merge.8.b.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.8.a.bcf /tmp/N9wvQi6tqJ/merge.8.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.9.a.vcf.gz /tmp/N9wvQi6tqJ/merge.9.b.vcf.gz
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.9.a.vcf.gz /tmp/N9wvQi6tqJ/merge.9.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version  /tmp/N9wvQi6tqJ/merge.9.a.bcf /tmp/N9wvQi6tqJ/merge.9.b.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob  /tmp/N9wvQi6tqJ/merge.9.a.bcf /tmp/N9wvQi6tqJ/merge.9.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.9.a.vcf.gz /tmp/N9wvQi6tqJ/merge.9.b.vcf.gz
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.9.a.vcf.gz /tmp/N9wvQi6tqJ/merge.9.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.9.a.bcf /tmp/N9wvQi6tqJ/merge.9.b.bcf
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/N9wvQi6tqJ/merge.9.a.bcf /tmp/N9wvQi6tqJ/merge.9.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
108s .. ok
108s 
108s test_vcf_merge:
108s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m none /tmp/N9wvQi6tqJ/merge.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.10.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m none /tmp/N9wvQi6tqJ/merge.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m none /tmp/N9wvQi6tqJ/merge.10.a.bcf /tmp/N9wvQi6tqJ/merge.10.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m none /tmp/N9wvQi6tqJ/merge.10.a.bcf /tmp/N9wvQi6tqJ/merge.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m both /tmp/N9wvQi6tqJ/merge.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.10.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m both /tmp/N9wvQi6tqJ/merge.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m both /tmp/N9wvQi6tqJ/merge.10.a.bcf /tmp/N9wvQi6tqJ/merge.10.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m both /tmp/N9wvQi6tqJ/merge.10.a.bcf /tmp/N9wvQi6tqJ/merge.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m snp-ins-del /tmp/N9wvQi6tqJ/merge.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.10.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m snp-ins-del /tmp/N9wvQi6tqJ/merge.10.a.vcf.gz /tmp/N9wvQi6tqJ/merge.10.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -m snp-ins-del /tmp/N9wvQi6tqJ/merge.10.a.bcf /tmp/N9wvQi6tqJ/merge.10.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob -m snp-ins-del /tmp/N9wvQi6tqJ/merge.10.a.bcf /tmp/N9wvQi6tqJ/merge.10.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.mrules.1.a.vcf.gz /tmp/N9wvQi6tqJ/merge.mrules.1.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.mrules.1.a.vcf.gz /tmp/N9wvQi6tqJ/merge.mrules.1.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.mrules.1.a.bcf /tmp/N9wvQi6tqJ/merge.mrules.1.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.mrules.1.a.bcf /tmp/N9wvQi6tqJ/merge.mrules.1.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/N9wvQi6tqJ/merge.mrules.1.a.vcf.gz /tmp/N9wvQi6tqJ/merge.mrules.1.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/N9wvQi6tqJ/merge.mrules.1.a.vcf.gz /tmp/N9wvQi6tqJ/merge.mrules.1.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/N9wvQi6tqJ/merge.mrules.1.a.bcf /tmp/N9wvQi6tqJ/merge.mrules.1.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/N9wvQi6tqJ/merge.mrules.1.a.bcf /tmp/N9wvQi6tqJ/merge.mrules.1.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.5.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.5.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.5.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.5.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.5.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.5.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.5.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.5.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - --merge none /tmp/N9wvQi6tqJ/merge.gvcf.5.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.5.b.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/N9wvQi6tqJ/merge.gvcf.5.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.5.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - --merge none /tmp/N9wvQi6tqJ/merge.gvcf.5.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.5.b.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/N9wvQi6tqJ/merge.gvcf.5.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.5.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.11.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.11.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.11.c.vcf.gz
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.11.a.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.11.b.vcf.gz /tmp/N9wvQi6tqJ/merge.gvcf.11.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.11.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.11.b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.11.c.bcf
109s .. ok
109s 
109s test_vcf_merge:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools merge --no-version -Ob --gvcf - /tmp/N9wvQi6tqJ/merge.gvcf.11.a.bcf /tmp/N9wvQi6tqJ/merge.gvcf.11.b.bcf /tmp/N9wvQi6tqJ/merge.gvcf.11.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version | grep -v ^##bcftools_
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/N9wvQi6tqJ/query.string.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.string.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/N9wvQi6tqJ/query.string.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.string.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/N9wvQi6tqJ/query.string.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.string.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.string.2.1.txt' /tmp/N9wvQi6tqJ/query.string.2.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.string.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.string.2.1.txt'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.string.2.2.txt' /tmp/N9wvQi6tqJ/query.string.2.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.string.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.string.2.2.txt'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%RSX\t%VKX\n' /tmp/N9wvQi6tqJ/query.variantkey.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.variantkey.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%RSX\t%VKX\n'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/N9wvQi6tqJ/query.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/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/N9wvQi6tqJ/view.vectors.vcf.gz
109s .. ok
109s 
109s test_vcf_query:
109s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.vectors.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/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'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/N9wvQi6tqJ/query.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/N9wvQi6tqJ/query.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/N9wvQi6tqJ/query.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/N9wvQi6tqJ/query.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/N9wvQi6tqJ/query.2.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IINT="."'  -f'%POS %IINT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IINT="."'  -f'%POS %IINT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IINT="."'  -f'%POS %IINT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IINT="."'  -f'%POS %IINT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/N9wvQi6tqJ/filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/N9wvQi6tqJ/filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/N9wvQi6tqJ/filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/N9wvQi6tqJ/filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%LINE' /tmp/N9wvQi6tqJ/query.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%LINE'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter-type.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/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/N9wvQi6tqJ/filter-missing-floats.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter-missing-floats.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/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'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/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/N9wvQi6tqJ/filter-missing-floats.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter-missing-floats.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/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'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/N9wvQi6tqJ/missing.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/N9wvQi6tqJ/query.filter.2.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/N9wvQi6tqJ/filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/N9wvQi6tqJ/filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/N9wvQi6tqJ/view.filter.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.filter.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/N9wvQi6tqJ/query.filter.3.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"' /tmp/N9wvQi6tqJ/query.filter.3.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/N9wvQi6tqJ/query.filter.3.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/N9wvQi6tqJ/filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/N9wvQi6tqJ/query.filter.4.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%ID\n' -i 'ID=@/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.56.out' /tmp/N9wvQi6tqJ/view.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/view.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%ID\n' -i 'ID=@/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.56.out'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/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/N9wvQi6tqJ/query.filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/N9wvQi6tqJ/query.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/N9wvQi6tqJ/query.negative.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.negative.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/N9wvQi6tqJ/query.negative.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.negative.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/N9wvQi6tqJ/query.negative.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.negative.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/N9wvQi6tqJ/query.negative.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.negative.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/N9wvQi6tqJ/query.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1'
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz
110s .. ok
110s 
110s test_vcf_query:
110s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/N9wvQi6tqJ/query.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/N9wvQi6tqJ/query.filter.6.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.6.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.7.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/N9wvQi6tqJ/query.filter.8.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.8.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/N9wvQi6tqJ/query.filter.8.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.8.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/N9wvQi6tqJ/query.filter.9.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.9.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/N9wvQi6tqJ/query.filter.9.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.9.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/N9wvQi6tqJ/query.filter.13.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.13.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/N9wvQi6tqJ/query.filter.10.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.10.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/N9wvQi6tqJ/query.filter.10.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.10.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/N9wvQi6tqJ/query.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/N9wvQi6tqJ/query.filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/N9wvQi6tqJ/query.filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt /tmp/N9wvQi6tqJ/query.smpl.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.smpl.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -l -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt /tmp/N9wvQi6tqJ/query.smpl.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.smpl.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -l -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f "[%SAMPLE %GT\n]" -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt /tmp/N9wvQi6tqJ/query.smpl.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.smpl.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f "[%SAMPLE %GT\n]" -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -l -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt /tmp/N9wvQi6tqJ/query.smpl.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.smpl.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -l -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.11.txt
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.txt /tmp/N9wvQi6tqJ/query.smpl.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.smpl.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.txt
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -l -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.txt /tmp/N9wvQi6tqJ/query.smpl.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.smpl.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -l -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/query.smpl.txt
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/N9wvQi6tqJ/query.filter.id.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.id.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%ID\n' -i'ID~"s12"'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/N9wvQi6tqJ/query.filter.id.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.filter.id.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%ID\n' -i'ID="rs123"'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/N9wvQi6tqJ/filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="A"' -f'%FILTER\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/N9wvQi6tqJ/filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER~"A"' -f'%FILTER\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/N9wvQi6tqJ/filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER="A;B"' -f'%FILTER\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/N9wvQi6tqJ/filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/N9wvQi6tqJ/filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/N9wvQi6tqJ/filter.12.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.12.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/N9wvQi6tqJ/filter.10.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.10.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'DP%10==2' -f'[ %DP]\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/N9wvQi6tqJ/filter.13.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/filter.13.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]' /tmp/N9wvQi6tqJ/query.header.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.header.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n' /tmp/N9wvQi6tqJ/query.header.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.header.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/N9wvQi6tqJ/query.header.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.header.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/N9wvQi6tqJ/query.header.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.header.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/N9wvQi6tqJ/query.header.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.header.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n'
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/N9wvQi6tqJ/query.header.vcf.gz
111s .. ok
111s 
111s test_vcf_query:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/query.header.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]'
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -cx -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -cx -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m- /tmp/N9wvQi6tqJ/norm.split.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m- /tmp/N9wvQi6tqJ/norm.split.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m- /tmp/N9wvQi6tqJ/norm.split.2.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m- /tmp/N9wvQi6tqJ/norm.split.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m- --force /tmp/N9wvQi6tqJ/norm.split.3.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m- --force /tmp/N9wvQi6tqJ/norm.split.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m- /tmp/N9wvQi6tqJ/norm.split.4.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m- /tmp/N9wvQi6tqJ/norm.split.4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m- --keep-sum AD /tmp/N9wvQi6tqJ/norm.split.4.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m- --keep-sum AD /tmp/N9wvQi6tqJ/norm.split.4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m- -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.split.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m- -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.split.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m+ /tmp/N9wvQi6tqJ/norm.merge.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m+ /tmp/N9wvQi6tqJ/norm.merge.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m+ /tmp/N9wvQi6tqJ/norm.merge.2.vcf.gz
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m+ /tmp/N9wvQi6tqJ/norm.merge.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
111s .. ok
111s 
111s test_vcf_norm:
111s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m+ /tmp/N9wvQi6tqJ/norm.merge.3.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m+ /tmp/N9wvQi6tqJ/norm.merge.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m+ -s /tmp/N9wvQi6tqJ/norm.merge.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m+ -s /tmp/N9wvQi6tqJ/norm.merge.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -Nc s -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.setref.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -Nc s -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.setref.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.telomere.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.fa /tmp/N9wvQi6tqJ/norm.telomere.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d snps /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d snps /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d indels /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d indels /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d both /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d both /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d all /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d all /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d none /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d none /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d exact /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d exact /tmp/N9wvQi6tqJ/norm.rmdup.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d none /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d none /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d exact /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d exact /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d indels /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d indels /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d any /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d any /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d both /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d both /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -d snps /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -d snps /tmp/N9wvQi6tqJ/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -c s -a -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.2.fa /tmp/N9wvQi6tqJ/norm.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -c s -a -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.2.fa /tmp/N9wvQi6tqJ/norm.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -c s -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.iupac.fa /tmp/N9wvQi6tqJ/norm.iupac.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -c s -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.iupac.fa /tmp/N9wvQi6tqJ/norm.iupac.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -c s -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.3.fa /tmp/N9wvQi6tqJ/norm.3.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -c s -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.3.fa /tmp/N9wvQi6tqJ/norm.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC -m -any /tmp/N9wvQi6tqJ/atomize.split.1.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC -m -any /tmp/N9wvQi6tqJ/atomize.split.1.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.1.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.1.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.1.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.1.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --atom-overlaps . /tmp/N9wvQi6tqJ/atomize.split.3.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --atom-overlaps . /tmp/N9wvQi6tqJ/atomize.split.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.4.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/N9wvQi6tqJ/atomize.split.4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m +both /tmp/N9wvQi6tqJ/norm.4.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m +both /tmp/N9wvQi6tqJ/norm.4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m +any /tmp/N9wvQi6tqJ/norm.4.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m +any /tmp/N9wvQi6tqJ/norm.4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m - --multi-overlaps 0 /tmp/N9wvQi6tqJ/norm.5.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m - --multi-overlaps 0 /tmp/N9wvQi6tqJ/norm.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m - --multi-overlaps . /tmp/N9wvQi6tqJ/norm.5.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m - --multi-overlaps . /tmp/N9wvQi6tqJ/norm.5.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m -any /tmp/N9wvQi6tqJ/norm.m-any.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m -any /tmp/N9wvQi6tqJ/norm.m-any.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m -any /tmp/N9wvQi6tqJ/norm.phased-split.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m -any /tmp/N9wvQi6tqJ/norm.phased-split.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  -m +any /tmp/N9wvQi6tqJ/norm.phased-join.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  -m +any /tmp/N9wvQi6tqJ/norm.phased-join.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --old-rec-tag ORI -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.symbolic.fa /tmp/N9wvQi6tqJ/norm.symbolic.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --old-rec-tag ORI -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.symbolic.fa /tmp/N9wvQi6tqJ/norm.symbolic.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --old-rec-tag ORI -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.symbolic.fa /tmp/N9wvQi6tqJ/norm.symbolic.2.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --old-rec-tag ORI -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.symbolic.fa /tmp/N9wvQi6tqJ/norm.symbolic.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --old-rec-tag ORI -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.right-align.fa /tmp/N9wvQi6tqJ/norm.right-align.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --old-rec-tag ORI -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.right-align.fa /tmp/N9wvQi6tqJ/norm.right-align.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm --no-version  --old-rec-tag ORI -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.right-align.gff -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.right-align.fa /tmp/N9wvQi6tqJ/norm.right-align.vcf.gz
112s .. ok
112s 
112s test_vcf_norm:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools norm -Ob  --old-rec-tag ORI -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.right-align.gff -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/norm.right-align.fa /tmp/N9wvQi6tqJ/norm.right-align.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -HA /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz 
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -HAA /tmp/N9wvQi6tqJ/merge.gvcf.2.a.vcf.gz 
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1:1-2
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1:1-2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1:1,1:2
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1:1,1:2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1:1-1
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r 1:1-1 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1} | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}:1-2
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}:1-2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2
112s .. ok
112s 
112s test_vcf_view:
112s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}:1-1
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1}:1-1 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1} | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}:1-2
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}:1-1
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}-2
113s .. ok, expected non-zero status
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/weird-chr-names.vcf.gz -r {1:1-1}-2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok, expected non-zero status
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -f PASS -Xks NA00003 /tmp/N9wvQi6tqJ/view.vcf.gz -r20,Y
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -f PASS -Xks NA00003 /tmp/N9wvQi6tqJ/view.vcf.gz -r20,Y | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -xs NA00003 /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -xs NA00003 /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -p /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -p /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -P /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -P /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -Hu /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -GVsnps /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -GVsnps /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -s ^NA00003 /tmp/N9wvQi6tqJ/view.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -s ^NA00003 /tmp/N9wvQi6tqJ/view.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version  /tmp/N9wvQi6tqJ/view.omitgenotypes.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob  /tmp/N9wvQi6tqJ/view.omitgenotypes.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -G /tmp/N9wvQi6tqJ/view.omitgenotypes.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -G /tmp/N9wvQi6tqJ/view.omitgenotypes.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -HG /tmp/N9wvQi6tqJ/view.omitgenotypes.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -a /tmp/N9wvQi6tqJ/many.alleles.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -a /tmp/N9wvQi6tqJ/many.alleles.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -asA /tmp/N9wvQi6tqJ/view.vectors.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -asA /tmp/N9wvQi6tqJ/view.vectors.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -asB /tmp/N9wvQi6tqJ/view.vectors.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -asB /tmp/N9wvQi6tqJ/view.vectors.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -asA /tmp/N9wvQi6tqJ/view.vectors.2.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -asA /tmp/N9wvQi6tqJ/view.vectors.2.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i'TXT0="text"' /tmp/N9wvQi6tqJ/view.filter.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.chrs.tab /tmp/N9wvQi6tqJ/view.chrs.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.chrs.tab /tmp/N9wvQi6tqJ/view.chrs.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -i 'POS>=3062917' /tmp/N9wvQi6tqJ/filter.2.vcf.gz 1:3062917-3157410
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -i 'POS>=3062917' /tmp/N9wvQi6tqJ/filter.2.vcf.gz 1:3062917-3157410 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/N9wvQi6tqJ/idx.1.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/N9wvQi6tqJ/idx.2.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/idx.2.bed /tmp/N9wvQi6tqJ/idx.2.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/idx.3.bed /tmp/N9wvQi6tqJ/idx.3.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/idx.4.bed /tmp/N9wvQi6tqJ/idx.4.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -Ht 2 /tmp/N9wvQi6tqJ/view-t.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -Ht 3 /tmp/N9wvQi6tqJ/view-t.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/N9wvQi6tqJ/overlap.vcf.gz 
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.1.vcf -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.1.vcf     | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.1.vcf -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.2.vcf -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.2.vcf     | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.2.vcf -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.3.vcf -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.3.vcf     | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.4.vcf -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.4.vcf     | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.4.vcf -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.5.vcf -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.5.vcf     | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_64bit:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view /tmp/autopkgtest.RAARSc/build.NFP/src/test/view64bit.5.vcf -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -C5:nonmajor /tmp/N9wvQi6tqJ/view.minmaxac.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -c6:nonmajor /tmp/N9wvQi6tqJ/view.minmaxac.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -q0.3:major /tmp/N9wvQi6tqJ/view.minmaxac.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/N9wvQi6tqJ/view.filter.annovar.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/N9wvQi6tqJ/view.filter.annovar.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/N9wvQi6tqJ/view.filter.annovar.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -H -a /tmp/N9wvQi6tqJ/view-a.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.sites.txt /tmp/N9wvQi6tqJ/view.sites.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.sites.txt /tmp/N9wvQi6tqJ/view.sites.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.sites.txt.gz /tmp/N9wvQi6tqJ/view.sites.vcf.gz 
113s .. ok
113s 
113s test_vcf_view:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.sites.txt.gz /tmp/N9wvQi6tqJ/view.sites.vcf.gz  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
113s .. ok
113s 
113s test_vcf_head:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
113s .. ok
113s 
113s test_vcf_head:
113s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -h 0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -h 1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -h 5 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -h 22 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -h 23 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -n 0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -n 1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -n 5 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -h 5 -n 5 < /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_head2:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -s0 /tmp/N9wvQi6tqJ/mpileup.2.vcf.gz
114s .. ok
114s 
114s test_vcf_head2:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -Ob /tmp/N9wvQi6tqJ/mpileup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -s0
114s .. ok
114s 
114s test_vcf_head2:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -s1 /tmp/N9wvQi6tqJ/mpileup.2.vcf.gz
114s .. ok
114s 
114s test_vcf_head2:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -Ob /tmp/N9wvQi6tqJ/mpileup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -s1
114s .. ok
114s 
114s test_vcf_head2:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -s2 -h2 /tmp/N9wvQi6tqJ/mpileup.2.vcf.gz
114s .. ok
114s 
114s test_vcf_head2:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version -Ob /tmp/N9wvQi6tqJ/mpileup.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools head -s2 -h2
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mg0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mg0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.4.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.4.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.5.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.5.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.X.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.X.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ped /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.X.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ped /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.X.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.X.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.X.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.NA19213.NA19129.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.NA19213.NA19129.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.NA19213.NA19129.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.NA19213.NA19129.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.samples --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.samples --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.2.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.2.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.3.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.3.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.4.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.4.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.5.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.5.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.6.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.4.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.6.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.7.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.5.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.7.tab.gz -i /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.cals.1.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.cals.1.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.cals.1.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.cals.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.cals.2.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.cals.2.vcf
114s .. ok
114s 
114s test_vcf_call_cAls:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mA -C alleles -T /tmp/N9wvQi6tqJ/mpileup.cals.2.tab.gz  /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.cals.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -cv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -cv /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.X.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ped /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.X.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ped /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.X.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.ploidy -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.2.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/call-G.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv /tmp/autopkgtest.RAARSc/build.NFP/src/test/call-G.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/call-G.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.RAARSc/build.NFP/src/test/call-G.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -mv -F AN_POP,AC_POP /tmp/autopkgtest.RAARSc/build.NFP/src/test/call-G.2.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -mv -F AN_POP,AC_POP /tmp/autopkgtest.RAARSc/build.NFP/src/test/call-G.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -m -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.txt /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -m -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.txt /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call --no-version -m -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.txt -a GP,GQ /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.vcf
114s .. ok
114s 
114s test_vcf_call:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools call -Ob -m -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.txt -a GP,GQ /tmp/autopkgtest.RAARSc/build.NFP/src/test/call.af-fixation.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
114s .. ok
114s 
114s test_vcf_filter:
114s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'TXT0="text"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'TXT0="text"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'FMT/STR="XX"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'FMT/STR="XX"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S. -e'FMT/FILTER="aaa"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.2.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/view.filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -mx -g2 -G2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -mx -g2 -G2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'INFO/DP=19' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'INFO/DP=19' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'INFO/DP=19' -s XX /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'INFO/DP=19' -s XX /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'INFO/DP=19' -s XX -m+ /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'INFO/DP=19' -s XX -mx /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'INFO/DP=19' -s XX -m+x /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'FMT/GT="0/2"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'FMT/GT="0/2"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'FMT/GT="0/2"' -s XX /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'ALT="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'ALT="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -i 'FORMAT/TEST3<25' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.4.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -i 'FORMAT/TEST4<25' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.4.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="A"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="A"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="RR"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="RR"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="RA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="RA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="AR"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="AR"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="AA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="AA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="aA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="aA"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="Aa"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="Aa"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="HOM"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="HOM"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="HET"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="HET"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'GT="HAP"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'GT="HAP"' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%GT]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'AD[:1]=11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'AD[:1]=11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'AD[1:]=11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'AD[1:]=11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'FR[0:1]=11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%FR]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'FR[0:1]=11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%FR]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'AD[*]="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'AD[*]="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'AD[0:0]=="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'AD[0:0]=="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'AD[0:0]!="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'AD[0:0]!="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS[\t%AD]\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'QUAL=="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%QUAL\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'QUAL=="."' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\t%QUAL\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'N_PASS(DP>32)=1' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'N_PASS(DP>32)=1' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'F_PASS(DP>32)=0.5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'F_MISSING>=1/5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'F_MISSING>=1/5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'F_MISSING>=0.2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'F_MISSING>=0.2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%POS\n'
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -mx -s + -g2:mnp,indel,other /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.7.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.7.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'FORMAT/AO==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i 'QUAL/FMT/AD==55' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.9.vcf | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.9.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
115s .. ok
115s 
115s test_vcf_filter:
115s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i 'QUAL/INFO/AD==10' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.9.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.9.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -S . -e 'ABS(AO[1:])==2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.10.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_filter:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /tmp/autopkgtest.RAARSc/build.NFP/src/test/filter.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_sort:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools sort -m 0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/sort.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
116s .. ok
116s 
116s test_vcf_sort:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools sort -Ob -m 0 /tmp/autopkgtest.RAARSc/build.NFP/src/test/sort.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
116s .. ok
116s 
116s test_vcf_sort:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools sort -m 1000 /tmp/autopkgtest.RAARSc/build.NFP/src/test/sort.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
116s .. ok
116s 
116s test_vcf_sort:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools sort -Ob -m 1000 /tmp/autopkgtest.RAARSc/build.NFP/src/test/sort.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/regions.tab /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/regions.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/autopkgtest.RAARSc/build.NFP/src/test/regions.tab
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/autopkgtest.RAARSc/build.NFP/src/test/regions.tab /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/N9wvQi6tqJ/regions.tab.gz /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/regions.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/N9wvQi6tqJ/regions.tab.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/N9wvQi6tqJ/regions.tab.gz /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/N9wvQi6tqJ/regions.bed /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/regions.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/N9wvQi6tqJ/regions.bed
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/N9wvQi6tqJ/regions.bed /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/N9wvQi6tqJ/regions.bed.gz /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/regions.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/N9wvQi6tqJ/regions.bed.gz
116s .. ok
116s 
116s test_vcf_regions:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/N9wvQi6tqJ/regions.bed.gz /tmp/N9wvQi6tqJ/regions.vcf.gz
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate2.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.hdr -c CHROM,POS,-,T_STR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate2.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.hdr -c CHROM,POS,-,T_STR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate2.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.hdr -c CHROM,FROM,TO,T_STR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate2.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.hdr -c CHROM,FROM,TO,T_STR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/N9wvQi6tqJ/annotate.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/N9wvQi6tqJ/annotate.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   -x FORMAT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   -x FORMAT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots4.vcf.gz  -c +INFO /tmp/N9wvQi6tqJ/annotate4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots4.vcf.gz  -c +INFO /tmp/N9wvQi6tqJ/annotate4.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots4.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots4.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots10.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate10.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots10.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate10.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots11.vcf.gz  -c FMT /tmp/N9wvQi6tqJ/annotate11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots11.vcf.gz  -c FMT /tmp/N9wvQi6tqJ/annotate11.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
116s test_vcf_annotate:
116s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
116s .. ok
116s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/N9wvQi6tqJ/annotate2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots13.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.hdr -c CHROM,BEG,END,ABC /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots13.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.hdr -c CHROM,BEG,END,ABC /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots13.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots13.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots13.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots13.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate13.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   -x FILTER/XX,INFO/XX --force /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate14.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   -x FILTER/XX,INFO/XX --force /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate14.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate15.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate15.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate15.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate15.tab.gz -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate15.tab.gz  -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">' /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate15.tab.gz  -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">' /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate15.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   -x FILTER /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate16.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   -x FILTER /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate16.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate17.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate17.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate17.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate17.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate17.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate17.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/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.RAARSc/build.NFP/src/test/annotate18.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/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.RAARSc/build.NFP/src/test/annotate18.1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/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.RAARSc/build.NFP/src/test/annotate18.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/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.RAARSc/build.NFP/src/test/annotate18.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   -c INFO/FILTER:=FILTER /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate19.dst.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   -c INFO/FILTER:=FILTER /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate19.dst.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/N9wvQi6tqJ/annotate19.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate20.src.vcf.gz  -c  FMT/GT /tmp/N9wvQi6tqJ/annotate20.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate20.src.vcf.gz  -c  FMT/GT /tmp/N9wvQi6tqJ/annotate20.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate20.src.vcf.gz  -c +FMT/GT /tmp/N9wvQi6tqJ/annotate20.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate20.src.vcf.gz  -c +FMT/GT /tmp/N9wvQi6tqJ/annotate20.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate20.src.vcf.gz  -c -FMT/GT /tmp/N9wvQi6tqJ/annotate20.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate20.src.vcf.gz  -c -FMT/GT /tmp/N9wvQi6tqJ/annotate20.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.multi.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.multi.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/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.RAARSc/build.NFP/src/test/annotate.missing-append.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/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.RAARSc/build.NFP/src/test/annotate.missing-append.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate9.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate9.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   --rename-annots /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate21.txt /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate21.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   --rename-annots /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate21.txt /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate21.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/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.RAARSc/build.NFP/src/test/annotate21.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/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.RAARSc/build.NFP/src/test/annotate21.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/N9wvQi6tqJ/annotate22.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/N9wvQi6tqJ/annotate22.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate23.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate23.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate24.src.vcf.gz  -c XX /tmp/N9wvQi6tqJ/annotate24.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate24.src.vcf.gz  -c XX /tmp/N9wvQi6tqJ/annotate24.dst.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate25.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate25.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate26.tab.gz  -c CHROM,POS,~POS /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate26.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate26.tab.gz  -c CHROM,POS,~POS /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate26.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
117s .. ok
117s 
117s test_vcf_annotate:
117s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.missing.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.olap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.olap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.olap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.olap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.id.vcf.gz  -c ALT /tmp/N9wvQi6tqJ/annotate.id.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.id.vcf.gz  -c ALT /tmp/N9wvQi6tqJ/annotate.id.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.id.vcf.gz  -c +ALT /tmp/N9wvQi6tqJ/annotate.id.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.id.vcf.gz  -c +ALT /tmp/N9wvQi6tqJ/annotate.id.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/N9wvQi6tqJ/annotate.id.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/N9wvQi6tqJ/annotate.id.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/N9wvQi6tqJ/annotate.id.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/N9wvQi6tqJ/annotate.id.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate27.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate27.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate28.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate   -m XXX /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob   -m XXX /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots34.tab.gz  -c CHROM,FROM,TO,INFO/END -H '##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate in reference for SV">' /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate34.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots34.tab.gz  -c CHROM,FROM,TO,INFO/END -H '##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate in reference for SV">' /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate34.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -a /tmp/N9wvQi6tqJ/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /tmp/autopkgtest.RAARSc/build.NFP/src/test/annots-mark.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_annotate:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate -Ob -a /tmp/N9wvQi6tqJ/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /tmp/autopkgtest.RAARSc/build.NFP/src/test/annots-mark.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version   /tmp/N9wvQi6tqJ/concat.1.a.vcf.gz /tmp/N9wvQi6tqJ/concat.1.b.vcf.gz
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob   /tmp/N9wvQi6tqJ/concat.1.a.vcf.gz /tmp/N9wvQi6tqJ/concat.1.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version   /tmp/N9wvQi6tqJ/concat.1.a.bcf /tmp/N9wvQi6tqJ/concat.1.b.bcf
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob   /tmp/N9wvQi6tqJ/concat.1.a.bcf /tmp/N9wvQi6tqJ/concat.1.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -a  /tmp/N9wvQi6tqJ/concat.2.a.vcf.gz /tmp/N9wvQi6tqJ/concat.2.b.vcf.gz
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -a  /tmp/N9wvQi6tqJ/concat.2.a.vcf.gz /tmp/N9wvQi6tqJ/concat.2.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -a  /tmp/N9wvQi6tqJ/concat.2.a.bcf /tmp/N9wvQi6tqJ/concat.2.b.bcf
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -a  /tmp/N9wvQi6tqJ/concat.2.a.bcf /tmp/N9wvQi6tqJ/concat.2.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -aD  /tmp/N9wvQi6tqJ/concat.2.a.vcf.gz /tmp/N9wvQi6tqJ/concat.2.b.vcf.gz
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -aD  /tmp/N9wvQi6tqJ/concat.2.a.vcf.gz /tmp/N9wvQi6tqJ/concat.2.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -aD  /tmp/N9wvQi6tqJ/concat.2.a.bcf /tmp/N9wvQi6tqJ/concat.2.b.bcf
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -aD  /tmp/N9wvQi6tqJ/concat.2.a.bcf /tmp/N9wvQi6tqJ/concat.2.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.3.a.vcf.gz /tmp/N9wvQi6tqJ/concat.3.b.vcf.gz /tmp/N9wvQi6tqJ/concat.3.0.vcf.gz /tmp/N9wvQi6tqJ/concat.3.c.vcf.gz /tmp/N9wvQi6tqJ/concat.3.d.vcf.gz /tmp/N9wvQi6tqJ/concat.3.e.vcf.gz /tmp/N9wvQi6tqJ/concat.3.f.vcf.gz
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.3.a.vcf.gz /tmp/N9wvQi6tqJ/concat.3.b.vcf.gz /tmp/N9wvQi6tqJ/concat.3.0.vcf.gz /tmp/N9wvQi6tqJ/concat.3.c.vcf.gz /tmp/N9wvQi6tqJ/concat.3.d.vcf.gz /tmp/N9wvQi6tqJ/concat.3.e.vcf.gz /tmp/N9wvQi6tqJ/concat.3.f.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.3.a.bcf /tmp/N9wvQi6tqJ/concat.3.b.bcf /tmp/N9wvQi6tqJ/concat.3.0.bcf /tmp/N9wvQi6tqJ/concat.3.c.bcf /tmp/N9wvQi6tqJ/concat.3.d.bcf /tmp/N9wvQi6tqJ/concat.3.e.bcf /tmp/N9wvQi6tqJ/concat.3.f.bcf
118s .. ok
118s 
118s test_vcf_concat:
118s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.3.a.bcf /tmp/N9wvQi6tqJ/concat.3.b.bcf /tmp/N9wvQi6tqJ/concat.3.0.bcf /tmp/N9wvQi6tqJ/concat.3.c.bcf /tmp/N9wvQi6tqJ/concat.3.d.bcf /tmp/N9wvQi6tqJ/concat.3.e.bcf /tmp/N9wvQi6tqJ/concat.3.f.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
118s Random seed for test_naive_concat: 1890374813
118s .. ok
118s 
119s test_naive_concat:
119s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --naive-force /tmp/N9wvQi6tqJ/naive_concat.0.bcf /tmp/N9wvQi6tqJ/naive_concat.1.bcf /tmp/N9wvQi6tqJ/naive_concat.2.bcf /tmp/N9wvQi6tqJ/naive_concat.3.bcf /tmp/N9wvQi6tqJ/naive_concat.4.bcf /tmp/N9wvQi6tqJ/naive_concat.5.bcf /tmp/N9wvQi6tqJ/naive_concat.6.bcf /tmp/N9wvQi6tqJ/naive_concat.7.bcf /tmp/N9wvQi6tqJ/naive_concat.8.bcf /tmp/N9wvQi6tqJ/naive_concat.9.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
119s .. ok
119s 
119s test_naive_concat:
119s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --naive /tmp/N9wvQi6tqJ/naive_concat.0.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.1.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.2.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.3.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.4.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.5.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.6.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.7.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.8.vcf.gz /tmp/N9wvQi6tqJ/naive_concat.9.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -H
119s .. ok
119s 
119s test_vcf_concat:
119s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l  /tmp/N9wvQi6tqJ/concat.4.a.vcf.gz /tmp/N9wvQi6tqJ/concat.4.b.vcf.gz
119s .. ok
119s 
119s test_vcf_concat:
119s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l  /tmp/N9wvQi6tqJ/concat.4.a.vcf.gz /tmp/N9wvQi6tqJ/concat.4.b.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
119s .. ok
119s 
119s test_vcf_concat:
119s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l  /tmp/N9wvQi6tqJ/concat.4.a.bcf /tmp/N9wvQi6tqJ/concat.4.b.bcf
119s .. ok
119s 
119s test_vcf_concat:
119s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l  /tmp/N9wvQi6tqJ/concat.4.a.bcf /tmp/N9wvQi6tqJ/concat.4.b.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
119s .. ok
119s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.5.a.vcf.gz /tmp/N9wvQi6tqJ/concat.5.b.vcf.gz /tmp/N9wvQi6tqJ/concat.5.c.vcf.gz
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.5.a.vcf.gz /tmp/N9wvQi6tqJ/concat.5.b.vcf.gz /tmp/N9wvQi6tqJ/concat.5.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.5.a.bcf /tmp/N9wvQi6tqJ/concat.5.b.bcf /tmp/N9wvQi6tqJ/concat.5.c.bcf
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l --ligate-warn  /tmp/N9wvQi6tqJ/concat.5.a.bcf /tmp/N9wvQi6tqJ/concat.5.b.bcf /tmp/N9wvQi6tqJ/concat.5.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -l --ligate-force  /tmp/N9wvQi6tqJ/concat.5.a.bcf /tmp/N9wvQi6tqJ/concat.5.b.bcf /tmp/N9wvQi6tqJ/concat.5.c.bcf
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -l --ligate-force  /tmp/N9wvQi6tqJ/concat.5.a.bcf /tmp/N9wvQi6tqJ/concat.5.b.bcf /tmp/N9wvQi6tqJ/concat.5.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -G -a -D  /tmp/N9wvQi6tqJ/concat.5.a.vcf.gz /tmp/N9wvQi6tqJ/concat.5.b.vcf.gz /tmp/N9wvQi6tqJ/concat.5.c.vcf.gz
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -G -a -D  /tmp/N9wvQi6tqJ/concat.5.a.vcf.gz /tmp/N9wvQi6tqJ/concat.5.b.vcf.gz /tmp/N9wvQi6tqJ/concat.5.c.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat --no-version -G -a -D  /tmp/N9wvQi6tqJ/concat.5.a.bcf /tmp/N9wvQi6tqJ/concat.5.b.bcf /tmp/N9wvQi6tqJ/concat.5.c.bcf
120s .. ok
120s 
120s test_vcf_concat:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools concat -Ob -G -a -D  /tmp/N9wvQi6tqJ/concat.5.a.bcf /tmp/N9wvQi6tqJ/concat.5.b.bcf /tmp/N9wvQi6tqJ/concat.5.c.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.hdr /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.hdr | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.hdr /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.hdr | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.hdr /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.hdr | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples2 /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples2 /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples2 /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples2 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples3 /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples3 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples3 /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples3 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples3 /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples3 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples4 /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples4 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples4 /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples4 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples4 /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/reheader.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -s /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.samples4 | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.empty.hdr /tmp/autopkgtest.RAARSc/build.NFP/src/test/empty.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/autopkgtest.RAARSc/build.NFP/src/test/empty.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.empty.hdr | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.empty.hdr /tmp/N9wvQi6tqJ/empty.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/empty.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.empty.hdr | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.empty.hdr /tmp/N9wvQi6tqJ/empty.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	cat /tmp/N9wvQi6tqJ/empty.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.empty.hdr | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.fai /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.fai /tmp/N9wvQi6tqJ/reheader.2.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.fai /tmp/N9wvQi6tqJ/reheader.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.2.hdr -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.fai /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.2.hdr -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.fai /tmp/N9wvQi6tqJ/reheader.2.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -h /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.2.hdr -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.fai /tmp/N9wvQi6tqJ/reheader.2.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.3.fai /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.3.fai /tmp/N9wvQi6tqJ/reheader.3.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
120s test_vcf_reheader:
120s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools reheader -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/reheader.3.fai /tmp/N9wvQi6tqJ/reheader.3.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view --no-version
120s .. ok
120s 
121s test_rename_chrs:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate --rename-chrs /tmp/N9wvQi6tqJ/rename.map -Ov /tmp/N9wvQi6tqJ/annotate.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM\t%POS\n'
121s .. ok
121s 
121s test_rename_chrs:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate --rename-chrs /tmp/N9wvQi6tqJ/rename.map -Ob /tmp/N9wvQi6tqJ/annotate.bcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM\t%POS\n'
121s .. ok
121s 
121s test_rename_chrs:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate --rename-chrs /tmp/N9wvQi6tqJ/rename.map -Ov /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM\t%POS\n'
121s .. ok
121s 
121s test_rename_chrs:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools annotate --rename-chrs /tmp/N9wvQi6tqJ/rename.map -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/annotate.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%CHROM\t%POS\n'
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,.
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --vcf-ids /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --vcf-ids --3N6 /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --vcf-ids --3N6
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,-
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert  --vcf-ids -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert  --vcf-ids -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --3N6 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.3N6.gen,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --3N6 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.3N6.gen,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --tag PL /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --tag PL
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --tag PL /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --tag PL
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --vcf-ids /tmp/N9wvQi6tqJ/check.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --vcf-ids /tmp/N9wvQi6tqJ/check.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --3N6 /tmp/N9wvQi6tqJ/check.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --3N6
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --3N6 /tmp/N9wvQi6tqJ/check.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --3N6
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --3N6 --vcf-ids /tmp/N9wvQi6tqJ/check.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g -,. --3N6 --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --3N6 --vcf-ids /tmp/N9wvQi6tqJ/check.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/check.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -g .,- --3N6 --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h -,.,. /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h -,.,.
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h .,-,. /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h .,-,.
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h .,-,. --vcf-ids /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h .,-,. --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h .,.,- /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -h .,.,-
121s .. ok
121s 
121s test_vcf_convert_hls2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -H /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hls.gt.hap,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hls.gt.legend,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hls.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hls2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -H /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hls.gt.hap,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hls.gt.legend,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hls.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --haplegendsample -,.,. /tmp/N9wvQi6tqJ/convert.hap-missing.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.hap-missing.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --haplegendsample -,.,.
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample -,. /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample -,.
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample -,. --vcf-ids /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample -,. --vcf-ids
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample .,- /tmp/N9wvQi6tqJ/convert.vcf.gz
121s .. ok
121s 
121s test_vcf_convert:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample .,-
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.hap,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --hapsample2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.hap,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --vcf-ids --hapsample2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.ids.hap,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.samples | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_hs2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --vcf-ids --hapsample2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.ids.hap,/tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.hs.gt.samples -Ou | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##
121s .. ok
121s 
121s test_vcf_convert_gvcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa /tmp/N9wvQi6tqJ/convert.gvcf.vcf.gz
121s .. ok
121s 
121s test_vcf_convert_gvcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view -Ob /tmp/N9wvQi6tqJ/convert.gvcf.vcf.gz | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/gvcf.fa | grep -v ^##bcftools
121s .. ok
121s 
121s test_vcf_convert_tsv2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --no-version  -c ID,CHROM,POS,AA -s SAMPLE1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.23andme
121s .. ok
121s 
121s test_vcf_convert_tsv2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -Ou  -c ID,CHROM,POS,AA -s SAMPLE1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.23andme | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
121s .. ok
121s 
121s test_vcf_convert_tsv2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert --no-version  -c -,CHROM,POS,REF,ALT -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.tsv
121s .. ok
121s 
121s test_vcf_convert_tsv2vcf:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools convert -Ou  -c -,CHROM,POS,REF,ALT -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.RAARSc/build.NFP/src/test/convert.tsv | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view | grep -v ^##bcftools_
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab 
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab 
121s .. ok
121s 
121s test_vcf_consensus_chain:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab -c /tmp/N9wvQi6tqJ/consensus.1.chain.new >/dev/null; cat /tmp/N9wvQi6tqJ/consensus.1.chain.new
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab 
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab 
121s .. ok
121s 
121s test_vcf_consensus_chain:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab -c /tmp/N9wvQi6tqJ/consensus.2.chain.new >/dev/null; cat /tmp/N9wvQi6tqJ/consensus.2.chain.new
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -I -s - -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab 
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -I -s - -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab 
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -I -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab --mask-with X -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab --mask-with lc  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -I -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab --mask-with X -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab --mask-with lc  
121s .. ok
121s 
121s test_vcf_consensus_chain:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -I -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.tab -c /tmp/N9wvQi6tqJ/consensus.3.chain.new >/dev/null; cat /tmp/N9wvQi6tqJ/consensus.3.chain.new
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H 1  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H 1  
121s .. ok
121s 
121s test_vcf_consensus_chain:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H 1  -c /tmp/N9wvQi6tqJ/consensus.4.chain.new >/dev/null; cat /tmp/N9wvQi6tqJ/consensus.4.chain.new
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus2.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 1  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus2.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 1  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus2.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 2  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus2.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 2  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/empty.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s -  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/empty.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s -  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus3.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 2 -M "?"  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus3.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 2 -M "?"  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus3.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 2 -M "?" -p xx_  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus3.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -H 2 -M "?" -p xx_  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus4.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -s -  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus4.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -s -  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus5.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus5.fa --haplotype LA  
121s .. ok
121s 
121s test_vcf_consensus:
121s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus5.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus5.fa --haplotype LA  
121s .. ok
121s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus6.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus6.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus6.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus6.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 2  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 2  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 4  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 4  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 2pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 2pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 4pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 4pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 1  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 1  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 3  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 3  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 1pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 1pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 3pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus7.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus7.fa -H 3pIu  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a .  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a .  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -e 'MinDP>15'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -e 'MinDP>15'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -e 'MinDP<15'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus8.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -a . -e 'MinDP<15'  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.9.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.1.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.9.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.1.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.9.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.2.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.9.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.2.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.10.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.1.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.10.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.1.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.10.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.2.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.10.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.9.2.fa -H A  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.11.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.11.fa -s smpl  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.11.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.11.fa -s smpl  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.11.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.11.fa -s smpl -a N  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.11.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.11.fa -s smpl -a N  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.12.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.12.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.12.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.12.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.13.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.13.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.13.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.13.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.14.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.14.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.14.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.14.fa -s -  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.12.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.12.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.12.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
122s .. ok
122s 
122s test_vcf_consensus:
122s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.12.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
122s .. ok
122s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.15.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.15.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.16.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -I  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.16.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -s - -I  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.16.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H I  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.16.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.fa -H I  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.17.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -s - -M N -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.17.bed 
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.17.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus2.fa -s - -M N -m /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.17.bed 
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.18.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.18.fa -s -  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.18.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.18.fa -s -  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.19.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.19.fa -s -   
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.19.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.19.fa -s -   
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa -s -  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa -s -  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa   
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa   
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa -M . -s b  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa -M . -s b  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa -M . -s a  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.20.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.20.fa -M . -s a  
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.21.vcf.gz -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.21.fa   
123s .. ok
123s 
123s test_vcf_consensus:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools consensus /tmp/N9wvQi6tqJ/consensus.21.bcf    -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/consensus.21.fa   
123s .. ok
123s 
123s test_mpileup:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
123s .. ok
123s 
123s test_mpileup:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
123s .. ok
123s 
123s test_mpileup:
123s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -b /tmp/N9wvQi6tqJ/mpileup.bam.list --no-version | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob -b /tmp/N9wvQi6tqJ/mpileup.bam.urllist | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -b /tmp/N9wvQi6tqJ/mpileup.cram.list --no-version | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob -b /tmp/N9wvQi6tqJ/mpileup.cram.urllist | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
124s .. ok
124s 
124s test_mpileup:
124s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
125s .. ok
125s 
125s test_mpileup:
125s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
126s .. ok
126s 
126s test_mpileup:
126s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/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.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/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.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/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.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/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.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
127s .. ok
127s 
127s test_mpileup:
127s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
128s .. ok
128s 
128s test_mpileup:
128s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.9.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.9.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.9.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.9.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.9.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.9.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.10.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.10.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.10.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.10.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.10.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
129s .. ok
129s 
129s test_mpileup:
129s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.10.samples -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup  -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
130s .. ok
130s 
130s test_mpileup:
130s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
131s .. ok
131s 
131s test_mpileup:
131s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
132s .. ok
132s 
132s test_mpileup:
132s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -G /tmp/autopkgtest.RAARSc/build.NFP/src/test/mplp.11.rgs -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
133s .. ok
133s 
133s test_mpileup:
133s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.1.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
134s .. ok
134s 
134s test_mpileup:
134s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.cram | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
135s .. ok
135s 
135s test_mpileup:
135s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.1.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.1.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.1.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.2.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.2.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.2.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.3.fa /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.3.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_mpileup:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.3.fa -Ob /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.3.1.bam /tmp/autopkgtest.RAARSc/build.NFP/src/test/mpileup/annot-NMBZ.3.2.bam | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
136s .. ok
136s 
136s test_csq:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.gff3 /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
136s .. ok
136s 
136s test_csq:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.chr.gff3 /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
136s .. ok
136s 
136s test_csq:
136s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.2.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.2.gff --ncsq 64 /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.nchr.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq.ychr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000410009 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000410009/ENST00000410009.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000410009/ENST00000410009.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000410009/frameshift.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000410009 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000410009 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000368801.2/ENST00000368801.2.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000368801.2/start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000381157/ENST00000381157.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000381157/ENST00000381157.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000381157/haploid-diploid.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000382647/ENST00000382647.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000382647/ENST00000382647.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000542803/ENST00000542803.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000542803/ENST00000542803.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000542803/splice-region.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000542803/ENST00000542803.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000542803/ENST00000542803.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000542803/splice-region.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000301246/ENST00000301246.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000301246/ENST00000301246.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000301246/15bp-insert.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0002/EDUMMY0002.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0002/EDUMMY0002.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0002/boundaries.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000593942/ENST00000593942.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000593942/ENST00000593942.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000593942/last-codon-deletion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000413103/ENST00000413103.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000413103/ENST00000413103.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000413103/long-deletion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/frame3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/frame3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/frame2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/frame2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/frame1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/frame1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000528237/ENST00000528237.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000528237/ENST00000528237.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000557788/ENST00000557788.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000557788/ENST00000557788.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000557788/long-overlap-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000571540/ENST00000571540.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000571540/ENST00000571540.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000571540/nmd.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000000000 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000573314/ENST00000573314.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000573314/ENST00000573314.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000573314/ENST00000573314.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000573314/ENST00000573314.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000422159 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf  | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000373833/ENST00000373833.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000373833/ENST00000373833.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000373833/boundary-insertion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000373833/ENST00000373833.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000373833/ENST00000373833.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000373833/boundary-insertion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249/ENST00000318249.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249/ENST00000318249.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249/start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249/ENST00000318249.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249/ENST00000318249.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249/start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
137s .. ok
137s 
137s test_csq_real:
137s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000295641/ENST00000295641.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000295641/ENST00000295641.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000295641/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000295641/ENST00000295641.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000295641/ENST00000295641.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000295641/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0001/EDUMMY0001.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0001/EDUMMY0001.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0001/starts-with-1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0001/EDUMMY0001.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0001/EDUMMY0001.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0001/starts-with-1.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420670/ENST00000420670.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420670/ENST00000420670.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420670/segfault.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420670/ENST00000420670.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420670/ENST00000420670.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420670/start-stop-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000448695/ENST00000448695.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000448695/ENST00000448695.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000294661/ENST00000294661.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000294661/ENST00000294661.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000294661/non-coding-boundary.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000294661/ENST00000294661.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000294661/ENST00000294661.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000294661/non-coding-boundary.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0003/EDUMMY0003.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0003/EDUMMY0003.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EDUMMY0003/long-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000360372/ENST00000360372.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000360372/ENST00000360372.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000360372/mnp.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000256452/ENST00000256452.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000256452/ENST00000256452.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000256452/intron.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000390520/ENST00000390520.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000390520/ENST00000390520.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000390520/deletion-overlap.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000378322/ENST00000378322.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000378322/ENST00000378322.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000378322/end-overlap-tscript.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000378322/ENST00000378322.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000378322/ENST00000378322.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000378322/end-overlap-tscript.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000285021/ENST00000285021.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000285021/ENST00000285021.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000543077/ENST00000543077.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000543077/ENST00000543077.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000543077/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000543077/ENST00000543077.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000543077/ENST00000543077.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000543077/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520795/ENST00000520795.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520795/ENST00000520795.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520795/long-inside-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520795/ENST00000520795.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520795/ENST00000520795.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520795/long-inside-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/snps.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/snps.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/insert3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000423372/insert3.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249.2/ENST00000318249.2.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000409523/ENST00000409523.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000409523/ENST00000409523.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000409523/long-overlapping-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000580206 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf  | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000218032/start-lost-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000368801/ENST00000368801.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000368801/ENST00000368801.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000368801/compound-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000271583/ENST00000271583.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000271583/ENST00000271583.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000271583/splice-acceptor.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000379416 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf       | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf       | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf       | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf       | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf                 | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000357367/ENST00000357367.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000357367/ENST00000357367.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000357367/stop-retained.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSG00000173376/ENSG00000173376.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSG00000173376/ENSG00000173376.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSG00000173376/synon.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520868/ENST00000520868.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520868/ENST00000520868.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000520868/long-deletion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000536784/ENST00000536784.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000536784/ENST00000536784.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000536784/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000536784/ENST00000536784.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000536784/ENST00000536784.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000536784/not-a-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000400151/ENST00000400151.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000400151/ENST00000400151.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000400151/long-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EMN908947 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/EMN908947 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000479739/ENST00000479739.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000479739/ENST00000479739.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000479739/short-cds-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000479739/ENST00000479739.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000479739/ENST00000479739.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000479739/short-cds-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000230048/ENST00000230048.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000230048/ENST00000230048.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000230048/start-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000519442/ENST00000519442.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000519442/ENST00000519442.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000519442/synon-splice-region-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000518414/ENST00000518414.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000518414/ENST00000518414.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000227471/ENST00000227471.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000227471/ENST00000227471.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
138s .. ok
138s 
138s test_csq_real:
138s 	cd /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENSMUST00000133836 && /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
138s .. ok
138s 
138s test_csq_real:
138s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000375992/ENST00000375992.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000375992/ENST00000375992.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000436063/ENST00000436063.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000436063/ENST00000436063.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000436063/insert-before-utr.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000545279/ENST00000545279.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000545279/ENST00000545279.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000545279/splice-region-insert.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000624631/ENST00000624631.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000624631/ENST00000624631.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000624631/ambiguous.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420190/ENST00000420190.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420190/ENST00000420190.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000420190/abort-in-csq-push.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000263103-INS/insertions.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000329454/ENST00000329454.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000329454/ENST00000329454.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000329454/boundary-deletion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000329454/ENST00000329454.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000329454/ENST00000329454.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000329454/boundary-deletion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000303039/ENST00000303039.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000303039/ENST00000303039.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000303039/not-a-stop.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -l -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000303039/ENST00000303039.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000303039/ENST00000303039.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000303039/not-a-stop.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_csq_real:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools csq -f /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000269081/ENST00000269081.fa -g /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000269081/ENST00000269081.gff /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /tmp/autopkgtest.RAARSc/build.NFP/src/test/csq/sort-csq | /tmp/autopkgtest.RAARSc/build.NFP/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^#
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz -Or -G30 --AF-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.tab.gz| grep -v ^#
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz -Or -G30 --AF-file /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.tab.gz --ignore-homref| grep -v ^#
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^#
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^#
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^#
139s .. ok
139s 
139s test_roh:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools roh /tmp/autopkgtest.RAARSc/build.NFP/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^#
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u GT,GT /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u GT,PL /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u PL,GT /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u PL,PL /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -p s1,s1 /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 /tmp/N9wvQi6tqJ/gtcheck.2.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0  /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/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/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.RAARSc/build.NFP/src/test/gtcheck.3.pairs /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u PL /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 --n-matches 4 /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO  | sort
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -p B,C,B,D /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u GT,GT -H /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u GT,PL -H /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u PL,GT -H /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -u PL,PL -H /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.RAARSc/build.NFP/src/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/N9wvQi6tqJ/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.RAARSc/build.NFP/src/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/N9wvQi6tqJ/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -u GT -e 30 /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -u GT -e 300 /tmp/N9wvQi6tqJ/gtcheck.1.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -u PL -e 30 /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck  /tmp/N9wvQi6tqJ/gtcheck.ntop.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck --n-matches 2 /tmp/N9wvQi6tqJ/gtcheck.ntop.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck  /tmp/N9wvQi6tqJ/gtcheck.5.vcf.gz -g /tmp/N9wvQi6tqJ/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -p A,B,B,C /tmp/N9wvQi6tqJ/gtcheck.6.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s test_gtcheck:
139s 	/tmp/autopkgtest.RAARSc/build.NFP/src/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/N9wvQi6tqJ/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
139s .. ok
139s 
139s 
139s Number of tests:
139s     total   .. 1662
139s     passed  .. 1662
139s     failed  .. 0
139s 
139s mv: cannot stat 'bcftools.orig': No such file or directory
140s autopkgtest [02:39:15]: test command1: -----------------------]
140s command1             PASS
140s autopkgtest [02:39:15]: test command1:  - - - - - - - - - - results - - - - - - - - - -
141s autopkgtest [02:39:16]: @@@@@@@@@@@@@@@@@@@@ summary
141s command1             PASS
152s Creating nova instance adt-noble-arm64-bcftools-20240327-023654-juju-7f2275-prod-proposed-migration-environment-3-a62d65d0-7fa3-46e9-bddb-fa0a37b43ee6 from image adt/ubuntu-noble-arm64-server-20240327.img (UUID 4cac5f13-6ada-4e25-827f-1de2aa2ec4b4)...