0s autopkgtest [19:11:25]: starting date and time: 2024-03-22 19:11:25+0000
  0s autopkgtest [19:11:25]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [19:11:25]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.49tghp3r/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed --apt-upgrade bcftools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=bcftools/1.19-1build1 curl/8.5.0-2ubuntu7 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' -- lxd -r lxd-armhf-10.44.124.165 lxd-armhf-10.44.124.165:autopkgtest/ubuntu/noble/armhf
 61s autopkgtest [19:12:26]: testbed dpkg architecture: armhf
 63s autopkgtest [19:12:28]: testbed apt version: 2.7.12
 63s autopkgtest [19:12:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 66s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 67s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4047 kB]
 76s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 76s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB]
 77s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [58.8 kB]
 77s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [640 kB]
 78s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B]
 78s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B]
 78s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B]
 78s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [4006 kB]
 81s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B]
 81s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [47.7 kB]
 82s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B]
 92s Fetched 9434 kB in 17s (560 kB/s)
 93s Reading package lists...
100s Get:1 http://ports.ubuntu.com/ubuntu-ports noble-proposed InRelease [117 kB]
101s Get:2 http://ports.ubuntu.com/ubuntu-ports noble-proposed/main armhf Packages [640 kB]
101s Get:3 http://ports.ubuntu.com/ubuntu-ports noble-proposed/main armhf c-n-f Metadata [2492 B]
101s Get:4 http://ports.ubuntu.com/ubuntu-ports noble-proposed/universe armhf Packages [4006 kB]
101s Get:5 http://ports.ubuntu.com/ubuntu-ports noble-proposed/universe armhf c-n-f Metadata [7776 B]
101s Get:6 http://ports.ubuntu.com/ubuntu-ports noble-proposed/restricted armhf Packages [1372 B]
101s Get:7 http://ports.ubuntu.com/ubuntu-ports noble-proposed/restricted armhf c-n-f Metadata [116 B]
101s Get:8 http://ports.ubuntu.com/ubuntu-ports noble-proposed/multiverse armhf Packages [47.7 kB]
101s Get:9 http://ports.ubuntu.com/ubuntu-ports noble-proposed/multiverse armhf c-n-f Metadata [116 B]
112s Fetched 4823 kB in 3s (1801 kB/s)
113s Reading package lists...
124s tee: /proc/self/fd/2: Permission denied
161s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble-proposed InRelease
161s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
161s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble InRelease
161s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease
161s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease
161s Hit:6 http://ftpmaster.internal/ubuntu noble-security InRelease
161s Hit:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease
161s Hit:8 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease
161s Hit:9 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease
168s Reading package lists...
168s Reading package lists...
169s Building dependency tree...
169s Reading state information...
171s Calculating upgrade...
172s The following packages were automatically installed and are no longer required:
172s   linux-headers-6.8.0-11 python3-lib2to3
172s Use 'apt autoremove' to remove them.
175s The following packages will be REMOVED:
175s   libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1
175s   libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11
175s   libhogweed6 libmagic1 libnetplan0 libnettle8 libnpth0 libnvme1 libparted2
175s   libpcap0.8 libperl5.38 libpng16-16 libpsl5 libreadline8 libreiserfscore0
175s   libssl3 libtirpc3 libuv1 linux-headers-6.8.0-11-generic python3-distutils
175s The following NEW packages will be installed:
175s   libapt-pkg6.0t64 libarchive13t64 libatm1t64 libcurl3t64-gnutls libcurl4t64
175s   libdb5.3t64 libelf1t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64
175s   libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64 libmagic1t64
175s   libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64
175s   libpcap0.8t64 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64
175s   libreiserfscore0t64 libssl3t64 libtirpc3t64 libuv1t64 linux-headers-6.8.0-20
175s   linux-headers-6.8.0-20-generic xdg-user-dirs
175s The following packages have been kept back:
175s   multipath-tools
175s The following packages will be upgraded:
175s   apparmor apt apt-utils bind9-dnsutils bind9-host bind9-libs binutils
175s   binutils-arm-linux-gnueabihf binutils-common bolt bsdextrautils bsdutils
175s   btrfs-progs cloud-init coreutils cryptsetup-bin curl dbus dbus-bin
175s   dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session
175s   debianutils dhcpcd-base dirmngr dmsetup dpkg dpkg-dev e2fsprogs
175s   e2fsprogs-l10n eject fdisk file fonts-ubuntu-console ftp fwupd gawk
175s   gcc-13-base gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg
175s   gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv
175s   groff-base ibverbs-providers inetutils-telnet info initramfs-tools
175s   initramfs-tools-bin initramfs-tools-core install-info iproute2 jq keyboxd
175s   kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils
175s   libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3
175s   libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3
175s   libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libbsd0 libc-bin libc6
175s   libcap-ng0 libcom-err2 libcryptsetup12 libctf-nobfd0 libctf0 libdbus-1-3
175s   libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libevent-core-2.1-7
175s   libexpat1 libfdisk1 libfido2-1 libftdi1-2 libfwupd2 libgcc-s1
175s   libgirepository-1.0-1 libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0
175s   libgusb2 libibverbs1 libjcat1 libjq1 libjson-glib-1.0-0
175s   libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3 libkrb5support0
175s   libldap-common libldap2 liblocale-gettext-perl liblzma5 libmagic-mgc
175s   libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14 libnsl2
175s   libnss-systemd libpam-modules libpam-modules-bin libpam-runtime
175s   libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0
175s   libpolkit-gobject-1-0 libprotobuf-c1 libpython3-stdlib libpython3.11-minimal
175s   libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libqmi-glib5
175s   libqmi-proxy libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules
175s   libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2
175s   libsframe1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6
175s   libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl
175s   libtirpc-common libudev1 libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1
175s   libxml2 libxmlb2 libxmuu1 linux-headers-generic locales logsave lshw lsof
175s   man-db mount mtr-tiny netplan-generator netplan.io openssh-client
175s   openssh-server openssh-sftp-server openssl parted perl perl-base
175s   perl-modules-5.38 pinentry-curses plymouth plymouth-theme-ubuntu-text psmisc
175s   python-apt-common python3 python3-apt python3-cryptography python3-dbus
175s   python3-gdbm python3-gi python3-lib2to3 python3-markupsafe python3-minimal
175s   python3-netplan python3-pkg-resources python3-pyrsistent python3-setuptools
175s   python3-typing-extensions python3-yaml python3.11 python3.11-minimal
175s   python3.12 python3.12-minimal readline-common rsync shared-mime-info sudo
175s   systemd systemd-dev systemd-resolved systemd-sysv systemd-timesyncd tcpdump
175s   telnet tnftp ubuntu-minimal ubuntu-pro-client ubuntu-pro-client-l10n
175s   ubuntu-standard udev udisks2 usb.ids util-linux uuid-runtime vim-common
175s   vim-tiny wget xxd xz-utils zlib1g
175s 240 upgraded, 32 newly installed, 31 to remove and 1 not upgraded.
175s Need to get 107 MB of archives.
175s After this operation, 84.4 MB of additional disk space will be used.
175s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu2 [102 kB]
175s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB]
175s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB]
175s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB]
176s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu6 [2827 kB]
177s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu2 [975 kB]
177s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu1 [49.2 kB]
177s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build6 [51.3 kB]
177s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12 armhf 3.12.2-4build3 [645 kB]
178s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1 armhf 2.6.1-2 [65.9 kB]
178s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-minimal armhf 3.12.2-4build3 [1942 kB]
178s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-stdlib armhf 3.12.2-4build3 [1906 kB]
179s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-minimal armhf 3.12.2-4build3 [816 kB]
179s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf parted armhf 3.6-3.1build2 [39.4 kB]
179s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu2 [160 kB]
179s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu1 [70.9 kB]
179s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu5 [103 kB]
179s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-timesyncd armhf 255.4-1ubuntu5 [36.0 kB]
179s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB]
179s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B]
179s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build1 [13.5 kB]
179s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1 [44.3 kB]
179s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu3 [62.0 kB]
179s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.0-0.2 [117 kB]
179s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB]
179s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudisks2-0 armhf 2.10.1-6 [143 kB]
179s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udisks2 armhf 2.10.1-6 [276 kB]
180s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf shared-mime-info armhf 2.4-1build1 [470 kB]
180s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-girepository-2.0 armhf 1.79.1-1ubuntu6 [24.8 kB]
180s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gir1.2-glib-2.0 armhf 2.79.3-3ubuntu5 [182 kB]
180s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgirepository-1.0-1 armhf 1.79.1-1ubuntu6 [106 kB]
180s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gi armhf 3.47.0-3build1 [219 kB]
180s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dbus armhf 1.3.2-5build2 [94.7 kB]
180s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpgme11t64 armhf 1.18.0-4.1ubuntu3 [120 kB]
180s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libvolume-key1 armhf 0.3.12-7build1 [38.4 kB]
180s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnetplan1 armhf 1.0-1 [113 kB]
180s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-netplan armhf 1.0-1 [22.5 kB]
180s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan-generator armhf 1.0-1 [58.7 kB]
180s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-bin armhf 0.142ubuntu23 [20.3 kB]
180s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools-core all 0.142ubuntu23 [50.1 kB]
180s Get:41 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-minimal armhf 1.536build1 [10.7 kB]
180s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf initramfs-tools all 0.142ubuntu23 [9058 B]
180s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf netplan.io armhf 1.0-1 [64.3 kB]
180s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmlb2 armhf 0.3.15-1build1 [57.0 kB]
180s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqrtr-glib0 armhf 1.2.2-1ubuntu3 [15.4 kB]
180s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-glib5 armhf 1.35.2-0ubuntu1 [908 kB]
180s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libqmi-proxy armhf 1.35.2-0ubuntu1 [5732 B]
180s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-agent-1-0 armhf 124-1ubuntu1 [15.3 kB]
180s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpolkit-gobject-1-0 armhf 124-1ubuntu1 [44.1 kB]
180s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-0t64 armhf 2.79.3-3ubuntu5 [1414 kB]
181s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjcat1 armhf 0.2.0-2build2 [30.4 kB]
181s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libarchive13t64 armhf 3.7.2-1.1ubuntu2 [330 kB]
181s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fwupd armhf 1.9.15-1 [4349 kB]
182s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client-l10n armhf 31.2.1 [19.4 kB]
182s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ubuntu-pro-client armhf 31.2.1 [216 kB]
182s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11 armhf 3.11.8-1build4 [589 kB]
182s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.11-minimal armhf 3.11.8-1build4 [1795 kB]
183s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-minimal armhf 3.11.8-1build4 [826 kB]
183s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-5ubuntu1 [19.0 kB]
183s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build2 [12.7 kB]
183s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build2 [8962 B]
183s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2 [1671 kB]
183s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu3 [15.0 kB]
183s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
184s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-gdbm armhf 3.12.2-3ubuntu2 [17.1 kB]
184s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-3build4 [1196 kB]
185s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1 [30.3 kB]
185s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1 [6208 B]
185s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2 [4101 kB]
186s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2 [231 kB]
186s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6 [661 kB]
186s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.11-stdlib armhf 3.11.8-1build4 [1810 kB]
187s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf keyboxd armhf 2.4.4-2ubuntu15 [111 kB]
187s Get:74 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1 [6940 B]
187s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu15 [224 kB]
187s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu15 [524 kB]
187s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-wks-client armhf 2.4.4-2ubuntu15 [87.4 kB]
187s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-utils armhf 2.4.4-2ubuntu15 [158 kB]
187s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu15 [235 kB]
187s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgsm armhf 2.4.4-2ubuntu15 [241 kB]
187s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-3.1build1 [129 kB]
187s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gawk armhf 1:5.2.1-2build2 [415 kB]
187s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf fdisk armhf 2.39.3-9ubuntu2 [135 kB]
187s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu15 [115 kB]
187s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dirmngr armhf 2.4.4-2ubuntu15 [346 kB]
188s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg all 2.4.4-2ubuntu15 [359 kB]
188s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-apt armhf 2.7.6build1 [162 kB]
188s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.13ubuntu1 [210 kB]
188s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.13ubuntu1 [986 kB]
188s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2 [187 kB]
188s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2 [187 kB]
188s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu2 [1046 kB]
188s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.13ubuntu1 [1367 kB]
189s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu7 [290 kB]
189s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfwupd2 armhf 1.9.15-1 [123 kB]
189s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.7 kB]
189s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf wget armhf 1.21.4-1ubuntu2 [317 kB]
189s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tnftp armhf 20230507-2build1 [98.6 kB]
189s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcap0.8t64 armhf 1.10.4-4.1ubuntu1 [137 kB]
189s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tcpdump armhf 4.99.4-3ubuntu2 [425 kB]
189s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB]
190s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-resolved armhf 255.4-1ubuntu5 [289 kB]
191s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sudo armhf 1.9.15p5-3ubuntu3 [936 kB]
192s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rsync armhf 3.2.7-1build1 [413 kB]
192s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-cryptography armhf 41.0.7-4build2 [788 kB]
193s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu11 [35.5 kB]
193s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-client armhf 1:9.6p1-3ubuntu11 [890 kB]
194s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssh-server armhf 1:9.6p1-3ubuntu11 [503 kB]
195s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB]
202s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-6.8.0-20-generic armhf 6.8.0-20.20 [1287 kB]
203s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-headers-generic armhf 6.8.0-20.20+1 [9610 B]
203s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu2 [1558 kB]
203s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB]
203s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB]
205s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf udev armhf 255.4-1ubuntu5 [1852 kB]
205s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB]
205s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnss-systemd armhf 255.4-1ubuntu5 [148 kB]
205s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-systemd armhf 255.4-1ubuntu5 [216 kB]
205s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB]
206s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu3 [47.0 kB]
206s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu3 [261 kB]
206s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB]
206s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-user-session armhf 1.14.10-4ubuntu2 [9962 B]
206s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu2 [45.0 kB]
206s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-bin armhf 1.14.10-4ubuntu2 [37.1 kB]
206s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB]
206s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus armhf 1.14.10-4ubuntu2 [28.1 kB]
206s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dbus-daemon armhf 1.14.10-4ubuntu2 [109 kB]
206s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdbus-1-3 armhf 1.14.10-4ubuntu2 [190 kB]
206s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kmod armhf 31+20240202-2ubuntu4 [91.8 kB]
206s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu4 [44.9 kB]
206s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu2 [171 kB]
206s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu2 [49.5 kB]
206s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu2 [34.4 kB]
206s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu2 [238 kB]
206s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu2 [196 kB]
206s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu2 [134 kB]
206s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu2 [135 kB]
206s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libparted2t64 armhf 3.6-3.1build2 [143 kB]
206s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu1 [599 kB]
207s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB]
207s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu2 [117 kB]
207s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-3.1build1 [56.5 kB]
207s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-yaml armhf 6.0.1-2build1 [117 kB]
207s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python-apt-common all 2.7.6build1 [19.8 kB]
207s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB]
207s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB]
207s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu4 [1229 kB]
208s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-minimal armhf 3.12.2-0ubuntu1 [27.1 kB]
208s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3 armhf 3.12.2-0ubuntu1 [24.1 kB]
208s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-stdlib armhf 3.12.2-0ubuntu1 [9802 B]
208s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu2 [78.7 kB]
208s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build1 [946 kB]
208s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-5ubuntu1 [49.7 kB]
208s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-utils3 armhf 3.1.0-1build1 [16.9 kB]
208s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-crypto3 armhf 3.1.0-1build1 [20.3 kB]
208s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB]
208s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dhcpcd-base armhf 1:10.0.6-1ubuntu2 [186 kB]
208s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf eject armhf 2.39.3-9ubuntu2 [43.2 kB]
208s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbpf1 armhf 1:1.3.0-2build1 [146 kB]
208s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf iproute2 armhf 6.1.0-1ubuntu5 [1060 kB]
209s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build2 [49.9 kB]
209s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1 [8018 B]
209s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lsof armhf 4.95.0-1build2 [248 kB]
209s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build2 [36.5 kB]
209s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-5.1ubuntu1 [119 kB]
209s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-5.1ubuntu1 [321 kB]
209s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-5.1ubuntu1 [31.4 kB]
209s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-5.1ubuntu1 [78.6 kB]
209s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu2 [21.9 kB]
209s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1 [73.2 kB]
209s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu6 [530 kB]
210s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf locales all 2.39-0ubuntu6 [4232 kB]
213s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-tiny armhf 2:9.1.0016-1ubuntu5 [665 kB]
213s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main armhf vim-common all 2:9.1.0016-1ubuntu5 [385 kB]
213s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B]
213s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-fs3 armhf 3.1.0-1build1 [34.4 kB]
214s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreiserfscore0t64 armhf 1:3.6.27-7.1 [66.2 kB]
214s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf btrfs-progs armhf 6.6.3-1.1build1 [852 kB]
214s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu2 [201 kB]
214s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu2 [571 kB]
215s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-loop3 armhf 3.1.0-1build1 [6502 B]
215s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-mdraid3 armhf 3.1.0-1build1 [13.3 kB]
215s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-nvme3 armhf 3.1.0-1build1 [17.5 kB]
215s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnvme1t64 armhf 1.8-3 [67.5 kB]
215s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-part3 armhf 3.1.0-1build1 [16.4 kB]
215s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev-swap3 armhf 3.1.0-1build1 [8894 B]
215s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblockdev3 armhf 3.1.0-1build1 [42.9 kB]
215s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgudev-1.0-0 armhf 1:238-3ubuntu2 [13.6 kB]
215s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu2 [595 kB]
215s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-proxy armhf 1.31.2-0ubuntu2 [5748 B]
215s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmbim-glib4 armhf 1.31.2-0ubuntu2 [216 kB]
216s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-common all 1.8.0-2build1 [4210 B]
216s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-glib-1.0-0 armhf 1.8.0-2build1 [61.2 kB]
216s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libusb-1.0-0 armhf 2:1.0.27-1 [48.7 kB]
216s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgusb2 armhf 0.4.8-1build1 [34.6 kB]
216s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmm-glib0 armhf 1.23.4-0ubuntu1 [214 kB]
216s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libprotobuf-c1 armhf 1.4.1-1ubuntu3 [17.7 kB]
216s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB]
216s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build1 [68.1 kB]
216s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB]
216s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libibverbs1 armhf 50.0-2build1 [57.9 kB]
217s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfido2-1 armhf 1.14.0-1build1 [75.8 kB]
217s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu3 [1280 kB]
218s Get:205 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.17 [88.9 kB]
218s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu2 [1216 kB]
219s Get:207 http://ftpmaster.internal/ubuntu noble-proposed/main armhf curl armhf 8.5.0-2ubuntu7 [219 kB]
219s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcurl4t64 armhf 8.5.0-2ubuntu7 [296 kB]
219s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3 [21.1 kB]
219s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3 [307 kB]
219s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3 [81.4 kB]
219s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libplymouth5 armhf 24.004.60-1ubuntu6 [140 kB]
219s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-3 [166 kB]
219s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-host armhf 1:9.18.24-0ubuntu3 [47.4 kB]
219s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-dnsutils armhf 1:9.18.24-0ubuntu3 [149 kB]
219s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bind9-libs armhf 1:9.18.24-0ubuntu3 [1148 kB]
220s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuv1t64 armhf 1.48.0-1.1 [82.9 kB]
220s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu2 [41.7 kB]
220s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu2 [10.8 kB]
220s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build4 [10.1 kB]
220s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB]
220s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf install-info armhf 7.1-3build1 [60.5 kB]
220s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-19ubuntu1 [47.7 kB]
220s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu2 [14.7 kB]
220s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dmsetup armhf 2:1.02.185-3ubuntu2 [81.1 kB]
220s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-5.1ubuntu1 [13.9 kB]
220s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbsd0 armhf 0.12.1-1 [36.6 kB]
220s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
220s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libslang2 armhf 2.3.3-3build1 [478 kB]
220s Get:230 http://ftpmaster.internal/ubuntu noble/main armhf xdg-user-dirs armhf 0.18-1 [17.3 kB]
220s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xxd armhf 2:9.1.0016-1ubuntu5 [62.4 kB]
220s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apparmor armhf 4.0.0-beta3-0ubuntu2 [562 kB]
220s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ftp all 20230507-2build1 [4724 B]
220s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main armhf inetutils-telnet armhf 2:2.5-3ubuntu3 [90.7 kB]
220s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main armhf info armhf 7.1-3build1 [127 kB]
220s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxmuu1 armhf 2:1.1.3-3build1 [8004 B]
220s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2build2 [310 kB]
220s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mtr-tiny armhf 0.95-1.1build1 [51.7 kB]
220s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu6 [9818 B]
220s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main armhf plymouth armhf 24.004.60-1ubuntu6 [142 kB]
220s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1 [176 kB]
220s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main armhf telnet all 0.17+2.5-3ubuntu3 [3682 B]
220s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.0-0.2 [271 kB]
220s Get:244 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-standard armhf 1.536build1 [10.7 kB]
220s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main armhf usb.ids all 2024.03.18-1 [223 kB]
220s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf-nobfd0 armhf 2.42-4ubuntu1 [88.0 kB]
220s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf0 armhf 2.42-4ubuntu1 [87.7 kB]
220s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu1 [2925 kB]
221s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbinutils armhf 2.42-4ubuntu1 [464 kB]
221s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils armhf 2.42-4ubuntu1 [3078 B]
221s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-common armhf 2.42-4ubuntu1 [217 kB]
221s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsframe1 armhf 2.42-4ubuntu1 [13.1 kB]
221s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bolt armhf 0.9.6-2build1 [138 kB]
221s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cryptsetup-bin armhf 2:2.7.0-1ubuntu2 [214 kB]
221s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu4 [1074 kB]
221s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu4 [268 kB]
221s Get:257 http://ftpmaster.internal/ubuntu noble/main armhf fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB]
221s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB]
221s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ibverbs-providers armhf 50.0-2build1 [27.4 kB]
221s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/main armhf jq armhf 1.7.1-3 [65.2 kB]
221s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjq1 armhf 1.7.1-3 [156 kB]
221s Get:262 http://ftpmaster.internal/ubuntu noble/main armhf libatm1t64 armhf 1:2.5.1-5.1 [20.0 kB]
221s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB]
221s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libftdi1-2 armhf 1.5-6build4 [25.7 kB]
221s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB]
221s Get:266 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules armhf 2.1.28+dfsg1-5ubuntu1 [61.3 kB]
221s Get:267 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-lib2to3 all 3.12.2-3ubuntu2 [79.3 kB]
221s Get:268 http://ftpmaster.internal/ubuntu noble/main armhf python3-markupsafe armhf 2.1.5-1build1 [12.1 kB]
221s Get:269 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-pyrsistent armhf 0.20.0-1build1 [53.0 kB]
221s Get:270 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-typing-extensions all 4.10.0-1 [60.7 kB]
221s Get:271 http://ftpmaster.internal/ubuntu noble/main armhf cloud-init all 24.1.2-0ubuntu1 [597 kB]
221s Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main armhf kpartx armhf 0.9.4-5ubuntu6 [31.5 kB]
227s Preconfiguring packages ...
228s Fetched 107 MB in 47s (2292 kB/s)
228s (Reading database ... 
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228s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_armhf.deb ...
228s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ...
228s Setting up bsdutils (1:2.39.3-9ubuntu2) ...
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228s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ...
228s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
228s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ...
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228s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ...
228s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
228s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ...
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229s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ...
229s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
229s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ...
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229s Preparing to unpack .../libc6_2.39-0ubuntu6_armhf.deb ...
230s Unpacking libc6:armhf (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
230s Setting up libc6:armhf (2.39-0ubuntu6) ...
231s (Reading database ... 
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231s Preparing to unpack .../openssl_3.0.13-0ubuntu2_armhf.deb ...
231s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
232s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_armhf.deb ...
232s Unpacking zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ...
232s Setting up zlib1g:armhf (1:1.3.dfsg-3.1ubuntu1) ...
232s (Reading database ... 
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232s Preparing to unpack .../0-librtmp1_2.4+20151223.gitfa8646d.1-2build6_armhf.deb ...
232s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ...
232s Preparing to unpack .../1-python3.12_3.12.2-4build3_armhf.deb ...
232s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ...
232s Preparing to unpack .../2-libexpat1_2.6.1-2_armhf.deb ...
232s Unpacking libexpat1:armhf (2.6.1-2) over (2.6.0-1) ...
233s Preparing to unpack .../3-python3.12-minimal_3.12.2-4build3_armhf.deb ...
233s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ...
233s Preparing to unpack .../4-libpython3.12-stdlib_3.12.2-4build3_armhf.deb ...
233s Unpacking libpython3.12-stdlib:armhf (3.12.2-4build3) over (3.12.2-1) ...
234s Preparing to unpack .../5-libpython3.12-minimal_3.12.2-4build3_armhf.deb ...
234s Unpacking libpython3.12-minimal:armhf (3.12.2-4build3) over (3.12.2-1) ...
234s Preparing to unpack .../6-parted_3.6-3.1build2_armhf.deb ...
234s Unpacking parted (3.6-3.1build2) over (3.6-3) ...
235s (Reading database ... 
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235s Removing libparted2:armhf (3.6-3) ...
235s (Reading database ... 
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235s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_armhf.deb ...
235s Unpacking libblkid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
235s Setting up libblkid1:armhf (2.39.3-9ubuntu2) ...
235s (Reading database ... 
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235s Preparing to unpack .../libselinux1_3.5-2ubuntu1_armhf.deb ...
235s Unpacking libselinux1:armhf (3.5-2ubuntu1) over (3.5-2build1) ...
235s Setting up libselinux1:armhf (3.5-2ubuntu1) ...
235s (Reading database ... 
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235s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ...
235s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
235s Preparing to unpack .../systemd-timesyncd_255.4-1ubuntu5_armhf.deb ...
235s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
236s Preparing to unpack .../dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ...
236s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
236s Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ...
236s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ...
236s Setting up libaudit-common (1:3.1.2-2.1) ...
236s (Reading database ... 
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236s Preparing to unpack .../libcap-ng0_0.8.4-2build1_armhf.deb ...
236s Unpacking libcap-ng0:armhf (0.8.4-2build1) over (0.8.4-2) ...
236s Setting up libcap-ng0:armhf (0.8.4-2build1) ...
236s (Reading database ... 
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236s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_armhf.deb ...
236s Unpacking libaudit1:armhf (1:3.1.2-2.1) over (1:3.1.2-2) ...
236s Setting up libaudit1:armhf (1:3.1.2-2.1) ...
236s (Reading database ... 
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236s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_armhf.deb ...
236s Unpacking libpam0g:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
236s Setting up libpam0g:armhf (1.5.3-5ubuntu3) ...
237s (Reading database ... 
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237s Preparing to unpack .../liblzma5_5.6.0-0.2_armhf.deb ...
237s Unpacking liblzma5:armhf (5.6.0-0.2) over (5.4.5-0.3) ...
237s Setting up liblzma5:armhf (5.6.0-0.2) ...
237s (Reading database ... 
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237s Preparing to unpack .../0-libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ...
237s Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
237s Preparing to unpack .../1-libudisks2-0_2.10.1-6_armhf.deb ...
237s Unpacking libudisks2-0:armhf (2.10.1-6) over (2.10.1-1ubuntu2) ...
237s Preparing to unpack .../2-udisks2_2.10.1-6_armhf.deb ...
237s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ...
238s Preparing to unpack .../3-shared-mime-info_2.4-1build1_armhf.deb ...
238s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ...
238s Preparing to unpack .../4-gir1.2-girepository-2.0_1.79.1-1ubuntu6_armhf.deb ...
238s Unpacking gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ...
238s Preparing to unpack .../5-gir1.2-glib-2.0_2.79.3-3ubuntu5_armhf.deb ...
238s Unpacking gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
238s Preparing to unpack .../6-libgirepository-1.0-1_1.79.1-1ubuntu6_armhf.deb ...
238s Unpacking libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) over (1.79.1-1) ...
238s Preparing to unpack .../7-python3-gi_3.47.0-3build1_armhf.deb ...
239s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ...
239s Preparing to unpack .../8-python3-dbus_1.3.2-5build2_armhf.deb ...
239s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ...
240s dpkg: libgpgme11:armhf: dependency problems, but removing anyway as you requested:
240s  libvolume-key1:armhf depends on libgpgme11 (>= 1.4.1).
240s  libjcat1:armhf depends on libgpgme11 (>= 1.2.0).
240s 
240s (Reading database ... 
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240s Removing libgpgme11:armhf (1.18.0-4ubuntu1) ...
240s Selecting previously unselected package libgpgme11t64:armhf.
240s (Reading database ... 
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240s Preparing to unpack .../00-libgpgme11t64_1.18.0-4.1ubuntu3_armhf.deb ...
240s Unpacking libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ...
240s Preparing to unpack .../01-libvolume-key1_0.3.12-7build1_armhf.deb ...
240s Unpacking libvolume-key1:armhf (0.3.12-7build1) over (0.3.12-5build2) ...
240s Selecting previously unselected package libnetplan1:armhf.
240s Preparing to unpack .../02-libnetplan1_1.0-1_armhf.deb ...
240s Unpacking libnetplan1:armhf (1.0-1) ...
240s Preparing to unpack .../03-python3-netplan_1.0-1_armhf.deb ...
240s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ...
240s Preparing to unpack .../04-netplan-generator_1.0-1_armhf.deb ...
240s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
240s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ...
240s Preparing to unpack .../05-initramfs-tools-bin_0.142ubuntu23_armhf.deb ...
240s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ...
240s Preparing to unpack .../06-initramfs-tools-core_0.142ubuntu23_all.deb ...
240s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ...
240s Preparing to unpack .../07-ubuntu-minimal_1.536build1_armhf.deb ...
240s Unpacking ubuntu-minimal (1.536build1) over (1.536) ...
241s Preparing to unpack .../08-initramfs-tools_0.142ubuntu23_all.deb ...
241s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ...
241s Preparing to unpack .../09-netplan.io_1.0-1_armhf.deb ...
241s Unpacking netplan.io (1.0-1) over (0.107.1-3) ...
241s Preparing to unpack .../10-libxmlb2_0.3.15-1build1_armhf.deb ...
241s Unpacking libxmlb2:armhf (0.3.15-1build1) over (0.3.15-1) ...
241s Preparing to unpack .../11-libqrtr-glib0_1.2.2-1ubuntu3_armhf.deb ...
241s Unpacking libqrtr-glib0:armhf (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ...
241s Preparing to unpack .../12-libqmi-glib5_1.35.2-0ubuntu1_armhf.deb ...
241s Unpacking libqmi-glib5:armhf (1.35.2-0ubuntu1) over (1.34.0-2) ...
241s Preparing to unpack .../13-libqmi-proxy_1.35.2-0ubuntu1_armhf.deb ...
241s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ...
241s Preparing to unpack .../14-libpolkit-agent-1-0_124-1ubuntu1_armhf.deb ...
241s Unpacking libpolkit-agent-1-0:armhf (124-1ubuntu1) over (124-1) ...
241s Preparing to unpack .../15-libpolkit-gobject-1-0_124-1ubuntu1_armhf.deb ...
241s Unpacking libpolkit-gobject-1-0:armhf (124-1ubuntu1) over (124-1) ...
242s (Reading database ... 
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242s Removing libnetplan0:armhf (0.107.1-3) ...
242s dpkg: libglib2.0-0:armhf: dependency problems, but removing anyway as you requested:
242s  libmm-glib0:armhf depends on libglib2.0-0 (>= 2.62.0).
242s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
242s  libmbim-glib4:armhf depends on libglib2.0-0 (>= 2.56).
242s  libjson-glib-1.0-0:armhf depends on libglib2.0-0 (>= 2.75.3).
242s  libjcat1:armhf depends on libglib2.0-0 (>= 2.75.3).
242s  libgusb2:armhf depends on libglib2.0-0 (>= 2.75.3).
242s  libgudev-1.0-0:armhf depends on libglib2.0-0 (>= 2.38.0).
242s  libfwupd2:armhf depends on libglib2.0-0 (>= 2.79.0).
242s  libblockdev3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-utils3:armhf depends on libglib2.0-0 (>= 2.75.3).
242s  libblockdev-swap3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-part3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-nvme3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-mdraid3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-loop3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-fs3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  libblockdev-crypto3:armhf depends on libglib2.0-0 (>= 2.42.2).
242s  fwupd depends on libglib2.0-0 (>= 2.79.0).
242s  bolt depends on libglib2.0-0 (>= 2.56.0).
242s 
242s Removing libglib2.0-0:armhf (2.79.2-1~ubuntu1) ...
242s Selecting previously unselected package libglib2.0-0t64:armhf.
242s (Reading database ... 
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242s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_armhf.deb ...
242s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:armhf.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
242s removed '/var/lib/dpkg/info/libglib2.0-0:armhf.postrm'
242s Unpacking libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ...
242s Preparing to unpack .../libjcat1_0.2.0-2build2_armhf.deb ...
242s Unpacking libjcat1:armhf (0.2.0-2build2) over (0.2.0-2) ...
242s dpkg: libarchive13:armhf: dependency problems, but removing anyway as you requested:
242s  fwupd depends on libarchive13 (>= 3.2.1).
242s 
242s (Reading database ... 
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242s Removing libarchive13:armhf (3.7.2-1ubuntu2) ...
242s Selecting previously unselected package libarchive13t64:armhf.
243s (Reading database ... 
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243s Preparing to unpack .../00-libarchive13t64_3.7.2-1.1ubuntu2_armhf.deb ...
243s Unpacking libarchive13t64:armhf (3.7.2-1.1ubuntu2) ...
243s Preparing to unpack .../01-fwupd_1.9.15-1_armhf.deb ...
243s Unpacking fwupd (1.9.15-1) over (1.9.14-1) ...
243s Preparing to unpack .../02-ubuntu-pro-client-l10n_31.2.1_armhf.deb ...
243s Unpacking ubuntu-pro-client-l10n (31.2.1) over (31.1) ...
243s Preparing to unpack .../03-ubuntu-pro-client_31.2.1_armhf.deb ...
244s Unpacking ubuntu-pro-client (31.2.1) over (31.1) ...
244s Preparing to unpack .../04-python3.11_3.11.8-1build4_armhf.deb ...
244s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ...
244s Preparing to unpack .../05-python3.11-minimal_3.11.8-1build4_armhf.deb ...
244s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ...
245s Preparing to unpack .../06-libpython3.11-minimal_3.11.8-1build4_armhf.deb ...
245s Unpacking libpython3.11-minimal:armhf (3.11.8-1build4) over (3.11.8-1) ...
245s Preparing to unpack .../07-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_armhf.deb ...
245s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
245s Preparing to unpack .../08-libtext-iconv-perl_1.7-8build2_armhf.deb ...
245s Unpacking libtext-iconv-perl:armhf (1.7-8build2) over (1.7-8build1) ...
245s Preparing to unpack .../09-libtext-charwidth-perl_0.04-11build2_armhf.deb ...
245s Unpacking libtext-charwidth-perl:armhf (0.04-11build2) over (0.04-11build1) ...
245s Preparing to unpack .../10-perl-base_5.38.2-3.2_armhf.deb ...
245s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
246s Setting up perl-base (5.38.2-3.2) ...
246s (Reading database ... 
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246s Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu3_armhf.deb ...
246s Unpacking liblocale-gettext-perl (1.07-6ubuntu3) over (1.07-6build1) ...
246s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
246s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
248s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu2_armhf.deb ...
248s Unpacking python3-gdbm:armhf (3.12.2-3ubuntu2) over (3.11.5-1) ...
248s Preparing to unpack .../man-db_2.12.0-3build4_armhf.deb ...
248s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ...
248s dpkg: libgdbm-compat4:armhf: dependency problems, but removing anyway as you requested:
248s  libperl5.38:armhf depends on libgdbm-compat4 (>= 1.18-3).
248s 
248s (Reading database ... 
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248s Removing libgdbm-compat4:armhf (1.23-5) ...
248s dpkg: libgdbm6:armhf: dependency problems, but removing anyway as you requested:
248s  libperl5.38:armhf depends on libgdbm6 (>= 1.21).
248s 
248s Removing libgdbm6:armhf (1.23-5) ...
248s Selecting previously unselected package libgdbm6t64:armhf.
249s (Reading database ... 
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249s Preparing to unpack .../libgdbm6t64_1.23-5.1_armhf.deb ...
249s Unpacking libgdbm6t64:armhf (1.23-5.1) ...
249s Selecting previously unselected package libgdbm-compat4t64:armhf.
249s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_armhf.deb ...
249s Unpacking libgdbm-compat4t64:armhf (1.23-5.1) ...
249s dpkg: libperl5.38:armhf: dependency problems, but removing anyway as you requested:
249s  perl depends on libperl5.38 (= 5.38.2-3).
249s 
249s (Reading database ... 
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249s Removing libperl5.38:armhf (5.38.2-3) ...
249s Selecting previously unselected package libperl5.38t64:armhf.
249s (Reading database ... 
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249s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_armhf.deb ...
249s Unpacking libperl5.38t64:armhf (5.38.2-3.2) ...
250s Preparing to unpack .../perl_5.38.2-3.2_armhf.deb ...
250s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ...
250s dpkg: libdb5.3:armhf: dependency problems, but removing anyway as you requested:
250s  libpython3.11-stdlib:armhf depends on libdb5.3.
250s  libpam-modules:armhf depends on libdb5.3.
250s  iproute2 depends on libdb5.3.
250s  apt-utils depends on libdb5.3.
250s 
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250s Removing libdb5.3:armhf (5.3.28+dfsg2-4) ...
250s Selecting previously unselected package libdb5.3t64:armhf.
250s (Reading database ... 
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250s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_armhf.deb ...
250s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-6) ...
250s Preparing to unpack .../libpython3.11-stdlib_3.11.8-1build4_armhf.deb ...
251s Unpacking libpython3.11-stdlib:armhf (3.11.8-1build4) over (3.11.8-1) ...
251s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_armhf.deb ...
251s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
251s dpkg: libnpth0:armhf: dependency problems, but removing anyway as you requested:
251s  gpgv depends on libnpth0 (>= 0.90).
251s  gpgsm depends on libnpth0 (>= 0.90).
251s  gpg-agent depends on libnpth0 (>= 0.90).
251s  gpg depends on libnpth0 (>= 0.90).
251s  dirmngr depends on libnpth0 (>= 0.90).
251s 
251s (Reading database ... 
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251s Removing libnpth0:armhf (1.6-3build2) ...
251s Selecting previously unselected package libnpth0t64:armhf.
251s (Reading database ... 
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251s Preparing to unpack .../libnpth0t64_1.6-3.1_armhf.deb ...
251s Unpacking libnpth0t64:armhf (1.6-3.1) ...
252s Setting up libnpth0t64:armhf (1.6-3.1) ...
252s (Reading database ... 
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252s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_armhf.deb ...
252s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
252s Setting up gpgv (2.4.4-2ubuntu15) ...
252s (Reading database ... 
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252s Preparing to unpack .../gpg_2.4.4-2ubuntu15_armhf.deb ...
252s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
252s Preparing to unpack .../gpg-wks-client_2.4.4-2ubuntu15_armhf.deb ...
252s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
252s Preparing to unpack .../gnupg-utils_2.4.4-2ubuntu15_armhf.deb ...
252s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
252s Preparing to unpack .../gpg-agent_2.4.4-2ubuntu15_armhf.deb ...
252s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
252s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_armhf.deb ...
252s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
252s dpkg: libreadline8:armhf: dependency problems, but removing anyway as you requested:
252s  gpgconf depends on libreadline8 (>= 6.0).
252s  gawk depends on libreadline8 (>= 6.0).
252s  fdisk depends on libreadline8 (>= 6.0).
252s 
253s (Reading database ... 
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253s Removing libreadline8:armhf (8.2-3) ...
253s Selecting previously unselected package libreadline8t64:armhf.
253s (Reading database ... 
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253s Preparing to unpack .../libreadline8t64_8.2-3.1build1_armhf.deb ...
253s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
253s Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
253s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
253s Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
253s Unpacking libreadline8t64:armhf (8.2-3.1build1) ...
253s Setting up libreadline8t64:armhf (8.2-3.1build1) ...
253s (Reading database ... 
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253s Preparing to unpack .../0-gawk_1%3a5.2.1-2build2_armhf.deb ...
253s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ...
253s Preparing to unpack .../1-fdisk_2.39.3-9ubuntu2_armhf.deb ...
253s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
253s Preparing to unpack .../2-gpgconf_2.4.4-2ubuntu15_armhf.deb ...
253s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
253s Preparing to unpack .../3-dirmngr_2.4.4-2ubuntu15_armhf.deb ...
253s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
254s Preparing to unpack .../4-gnupg_2.4.4-2ubuntu15_all.deb ...
254s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
254s Preparing to unpack .../5-python3-apt_2.7.6build1_armhf.deb ...
254s Unpacking python3-apt (2.7.6build1) over (2.7.6) ...
254s Preparing to unpack .../6-apt-utils_2.7.13ubuntu1_armhf.deb ...
254s Unpacking apt-utils (2.7.13ubuntu1) over (2.7.12) ...
254s dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested:
254s  apt depends on libapt-pkg6.0 (>= 2.7.12).
254s 
254s (Reading database ... 
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254s Removing libapt-pkg6.0:armhf (2.7.12) ...
254s dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested:
254s  libhogweed6:armhf depends on libnettle8.
254s  libgnutls30:armhf depends on libnettle8 (>= 3.9~).
254s  libcurl3-gnutls:armhf depends on libnettle8.
254s 
254s Removing libnettle8:armhf (3.9.1-2) ...
254s Selecting previously unselected package libapt-pkg6.0t64:armhf.
254s (Reading database ... 
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254s Preparing to unpack .../libapt-pkg6.0t64_2.7.13ubuntu1_armhf.deb ...
254s Unpacking libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ...
255s Setting up libapt-pkg6.0t64:armhf (2.7.13ubuntu1) ...
255s Selecting previously unselected package libnettle8t64:armhf.
255s (Reading database ... 
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255s Preparing to unpack .../libnettle8t64_3.9.1-2.2_armhf.deb ...
255s Unpacking libnettle8t64:armhf (3.9.1-2.2) ...
255s Setting up libnettle8t64:armhf (3.9.1-2.2) ...
255s dpkg: libhogweed6:armhf: dependency problems, but removing anyway as you requested:
255s  libgnutls30:armhf depends on libhogweed6 (>= 3.6).
255s 
255s (Reading database ... 
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255s Removing libhogweed6:armhf (3.9.1-2) ...
255s Selecting previously unselected package libhogweed6t64:armhf.
255s (Reading database ... 
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255s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_armhf.deb ...
255s Unpacking libhogweed6t64:armhf (3.9.1-2.2) ...
255s Setting up libhogweed6t64:armhf (3.9.1-2.2) ...
255s dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested:
255s  libcurl3-gnutls:armhf depends on libgnutls30 (>= 3.8.2).
255s  apt depends on libgnutls30 (>= 3.8.1).
255s 
255s (Reading database ... 
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256s Removing libgnutls30:armhf (3.8.3-1ubuntu1) ...
256s Selecting previously unselected package libgnutls30t64:armhf.
256s (Reading database ... 
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256s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_armhf.deb ...
256s Unpacking libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ...
256s Setting up libgnutls30t64:armhf (3.8.3-1.1ubuntu2) ...
256s (Reading database ... 
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256s Preparing to unpack .../apt_2.7.13ubuntu1_armhf.deb ...
256s Unpacking apt (2.7.13ubuntu1) over (2.7.12) ...
256s Setting up apt (2.7.13ubuntu1) ...
258s dpkg: libcurl3-gnutls:armhf: dependency problems, but removing anyway as you requested:
258s  libfwupd2:armhf depends on libcurl3-gnutls (>= 7.63.0).
258s 
258s (Reading database ... 
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258s Removing libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ...
258s Selecting previously unselected package libcurl3t64-gnutls:armhf.
258s (Reading database ... 
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259s Preparing to unpack .../libcurl3t64-gnutls_8.5.0-2ubuntu7_armhf.deb ...
259s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ...
259s Preparing to unpack .../libfwupd2_1.9.15-1_armhf.deb ...
259s Unpacking libfwupd2:armhf (1.9.15-1) over (1.9.14-1) ...
259s dpkg: libpsl5:armhf: dependency problems, but removing anyway as you requested:
259s  wget depends on libpsl5 (>= 0.16.0).
259s  libcurl4:armhf depends on libpsl5 (>= 0.16.0).
259s 
259s (Reading database ... 
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259s Removing libpsl5:armhf (0.21.2-1build1) ...
259s Selecting previously unselected package libpsl5t64:armhf.
259s (Reading database ... 
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259s Preparing to unpack .../libpsl5t64_0.21.2-1.1_armhf.deb ...
259s Unpacking libpsl5t64:armhf (0.21.2-1.1) ...
259s Preparing to unpack .../wget_1.21.4-1ubuntu2_armhf.deb ...
259s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ...
259s Preparing to unpack .../tnftp_20230507-2build1_armhf.deb ...
259s Unpacking tnftp (20230507-2build1) over (20230507-2) ...
259s dpkg: libpcap0.8:armhf: dependency problems, but removing anyway as you requested:
259s  tcpdump depends on libpcap0.8 (>= 1.9.1).
259s 
259s (Reading database ... 
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259s Removing libpcap0.8:armhf (1.10.4-4ubuntu3) ...
259s Selecting previously unselected package libpcap0.8t64:armhf.
260s (Reading database ... 
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260s Preparing to unpack .../00-libpcap0.8t64_1.10.4-4.1ubuntu1_armhf.deb ...
260s Unpacking libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ...
260s Preparing to unpack .../01-tcpdump_4.99.4-3ubuntu2_armhf.deb ...
260s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ...
260s Preparing to unpack .../02-libsystemd-shared_255.4-1ubuntu5_armhf.deb ...
260s Unpacking libsystemd-shared:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
260s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_armhf.deb ...
260s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
260s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_armhf.deb ...
260s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ...
260s Preparing to unpack .../05-rsync_3.2.7-1build1_armhf.deb ...
260s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ...
260s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_armhf.deb ...
261s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ...
261s Preparing to unpack .../07-openssh-sftp-server_1%3a9.6p1-3ubuntu11_armhf.deb ...
261s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
261s Preparing to unpack .../08-openssh-client_1%3a9.6p1-3ubuntu11_armhf.deb ...
261s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
261s Preparing to unpack .../09-openssh-server_1%3a9.6p1-3ubuntu11_armhf.deb ...
261s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
262s Selecting previously unselected package linux-headers-6.8.0-20.
262s Preparing to unpack .../10-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ...
262s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ...
274s Selecting previously unselected package linux-headers-6.8.0-20-generic.
274s Preparing to unpack .../11-linux-headers-6.8.0-20-generic_6.8.0-20.20_armhf.deb ...
274s Unpacking linux-headers-6.8.0-20-generic (6.8.0-20.20) ...
280s Preparing to unpack .../12-linux-headers-generic_6.8.0-20.20+1_armhf.deb ...
280s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ...
280s (Reading database ... 
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280s Removing linux-headers-6.8.0-11-generic (6.8.0-11.11) ...
282s dpkg: libssl3:armhf: dependency problems, but removing anyway as you requested:
282s  systemd depends on libssl3 (>= 3.0.0).
282s  libssh-4:armhf depends on libssl3 (>= 3.0.0).
282s  libsasl2-modules:armhf depends on libssl3 (>= 3.0.0).
282s  libsasl2-2:armhf depends on libssl3 (>= 3.0.0).
282s  libnvme1 depends on libssl3 (>= 3.0.0).
282s  libkrb5-3:armhf depends on libssl3 (>= 3.0.0).
282s  libkmod2:armhf depends on libssl3 (>= 3.0.0).
282s  libfido2-1:armhf depends on libssl3 (>= 3.0.0).
282s  libcurl4:armhf depends on libssl3 (>= 3.0.0).
282s  libcryptsetup12:armhf depends on libssl3 (>= 3.0.0).
282s  kmod depends on libssl3 (>= 3.0.0).
282s  dhcpcd-base depends on libssl3 (>= 3.0.0).
282s  bind9-libs:armhf depends on libssl3 (>= 3.0.0).
282s 
282s Removing libssl3:armhf (3.0.10-1ubuntu4) ...
282s Selecting previously unselected package libssl3t64:armhf.
282s (Reading database ... 
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282s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_armhf.deb ...
282s Unpacking libssl3t64:armhf (3.0.13-0ubuntu2) ...
282s Setting up libssl3t64:armhf (3.0.13-0ubuntu2) ...
282s (Reading database ... 
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282s Preparing to unpack .../libudev1_255.4-1ubuntu5_armhf.deb ...
282s Unpacking libudev1:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
283s Setting up libudev1:armhf (255.4-1ubuntu5) ...
283s (Reading database ... 
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283s Preparing to unpack .../systemd_255.4-1ubuntu5_armhf.deb ...
283s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
284s Preparing to unpack .../udev_255.4-1ubuntu5_armhf.deb ...
284s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
284s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_armhf.deb ...
284s Unpacking libsystemd0:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
284s Setting up libsystemd0:armhf (255.4-1ubuntu5) ...
284s Setting up libsystemd-shared:armhf (255.4-1ubuntu5) ...
284s Setting up systemd-dev (255.4-1ubuntu5) ...
284s Setting up systemd (255.4-1ubuntu5) ...
286s (Reading database ... 
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286s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_armhf.deb ...
286s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
286s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_armhf.deb ...
286s Unpacking libnss-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
286s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_armhf.deb ...
286s Unpacking libpam-systemd:armhf (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
286s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_armhf.deb ...
286s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
286s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ...
287s pam_namespace.service is a disabled or a static unit not running, not starting it.
287s (Reading database ... 
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287s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_armhf.deb ...
288s Unpacking libpam-modules:armhf (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
288s Setting up libpam-modules:armhf (1.5.3-5ubuntu3) ...
288s Installing new version of config file /etc/security/namespace.init ...
288s (Reading database ... 
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288s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ...
288s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
288s Setting up libpam-runtime (1.5.3-5ubuntu3) ...
289s (Reading database ... 
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289s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_armhf.deb ...
289s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
289s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_armhf.deb ...
289s Unpacking libapparmor1:armhf (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ...
289s Preparing to unpack .../2-dbus-bin_1.14.10-4ubuntu2_armhf.deb ...
289s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
289s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ...
289s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
289s Preparing to unpack .../4-dbus_1.14.10-4ubuntu2_armhf.deb ...
289s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
289s Preparing to unpack .../5-dbus-daemon_1.14.10-4ubuntu2_armhf.deb ...
289s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
290s Preparing to unpack .../6-libdbus-1-3_1.14.10-4ubuntu2_armhf.deb ...
290s Unpacking libdbus-1-3:armhf (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
290s Preparing to unpack .../7-kmod_31+20240202-2ubuntu4_armhf.deb ...
290s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
290s dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty
290s Preparing to unpack .../8-libkmod2_31+20240202-2ubuntu4_armhf.deb ...
290s Unpacking libkmod2:armhf (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
290s Preparing to unpack .../9-libmount1_2.39.3-9ubuntu2_armhf.deb ...
290s Unpacking libmount1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
290s Setting up libmount1:armhf (2.39.3-9ubuntu2) ...
290s (Reading database ... 
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290s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu2_armhf.deb ...
290s Unpacking libseccomp2:armhf (2.5.5-1ubuntu2) over (2.5.5-1ubuntu1) ...
290s Setting up libseccomp2:armhf (2.5.5-1ubuntu2) ...
290s (Reading database ... 
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290s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_armhf.deb ...
290s Unpacking libuuid1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
291s Setting up libuuid1:armhf (2.39.3-9ubuntu2) ...
291s (Reading database ... 
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291s Preparing to unpack .../0-libcryptsetup12_2%3a2.7.0-1ubuntu2_armhf.deb ...
291s Unpacking libcryptsetup12:armhf (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
291s Preparing to unpack .../1-libfdisk1_2.39.3-9ubuntu2_armhf.deb ...
291s Unpacking libfdisk1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
291s Preparing to unpack .../2-mount_2.39.3-9ubuntu2_armhf.deb ...
291s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
291s Preparing to unpack .../3-libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_armhf.deb ...
291s Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ...
291s Selecting previously unselected package libparted2t64:armhf.
291s Preparing to unpack .../4-libparted2t64_3.6-3.1build2_armhf.deb ...
291s Unpacking libparted2t64:armhf (3.6-3.1build2) ...
291s Preparing to unpack .../5-libsqlite3-0_3.45.1-1ubuntu1_armhf.deb ...
291s Unpacking libsqlite3-0:armhf (3.45.1-1ubuntu1) over (3.45.1-1) ...
291s Preparing to unpack .../6-pinentry-curses_1.2.1-3ubuntu4_armhf.deb ...
291s Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-3ubuntu1) ...
291s Preparing to unpack .../7-libsmartcols1_2.39.3-9ubuntu2_armhf.deb ...
291s Unpacking libsmartcols1:armhf (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
292s Setting up libsmartcols1:armhf (2.39.3-9ubuntu2) ...
292s (Reading database ... 
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292s Preparing to unpack .../0-readline-common_8.2-3.1build1_all.deb ...
292s Unpacking readline-common (8.2-3.1build1) over (8.2-3) ...
292s Preparing to unpack .../1-python3-yaml_6.0.1-2build1_armhf.deb ...
292s Unpacking python3-yaml (6.0.1-2build1) over (6.0.1-2) ...
292s Preparing to unpack .../2-python-apt-common_2.7.6build1_all.deb ...
292s Unpacking python-apt-common (2.7.6build1) over (2.7.6) ...
292s Preparing to unpack .../3-python3-setuptools_68.1.2-2ubuntu1_all.deb ...
293s Unpacking python3-setuptools (68.1.2-2ubuntu1) over (68.1.2-2) ...
293s Preparing to unpack .../4-python3-pkg-resources_68.1.2-2ubuntu1_all.deb ...
293s Unpacking python3-pkg-resources (68.1.2-2ubuntu1) over (68.1.2-2) ...
293s Preparing to unpack .../5-dpkg_1.22.6ubuntu4_armhf.deb ...
293s Unpacking dpkg (1.22.6ubuntu4) over (1.22.4ubuntu5) ...
294s Setting up dpkg (1.22.6ubuntu4) ...
295s Setting up libpython3.12-minimal:armhf (3.12.2-4build3) ...
295s Setting up libexpat1:armhf (2.6.1-2) ...
295s Setting up python3.12-minimal (3.12.2-4build3) ...
298s (Reading database ... 
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298s Preparing to unpack .../python3-minimal_3.12.2-0ubuntu1_armhf.deb ...
298s Unpacking python3-minimal (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
298s Setting up python3-minimal (3.12.2-0ubuntu1) ...
299s (Reading database ... 
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299s Preparing to unpack .../00-python3_3.12.2-0ubuntu1_armhf.deb ...
299s Unpacking python3 (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
299s Preparing to unpack .../01-libpython3-stdlib_3.12.2-0ubuntu1_armhf.deb ...
299s Unpacking libpython3-stdlib:armhf (3.12.2-0ubuntu1) over (3.12.1-0ubuntu2) ...
300s Preparing to unpack .../02-bsdextrautils_2.39.3-9ubuntu2_armhf.deb ...
300s Unpacking bsdextrautils (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
300s Preparing to unpack .../03-groff-base_1.23.0-3build1_armhf.deb ...
300s Unpacking groff-base (1.23.0-3build1) over (1.23.0-3) ...
300s Preparing to unpack .../04-libsasl2-2_2.1.28+dfsg1-5ubuntu1_armhf.deb ...
300s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
300s Preparing to unpack .../05-libblockdev-utils3_3.1.0-1build1_armhf.deb ...
300s Unpacking libblockdev-utils3:armhf (3.1.0-1build1) over (3.1.0-1) ...
300s Preparing to unpack .../06-libblockdev-crypto3_3.1.0-1build1_armhf.deb ...
300s Unpacking libblockdev-crypto3:armhf (3.1.0-1build1) over (3.1.0-1) ...
300s Preparing to unpack .../07-logsave_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
300s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
300s Preparing to unpack .../08-dhcpcd-base_1%3a10.0.6-1ubuntu2_armhf.deb ...
300s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ...
300s Preparing to unpack .../09-eject_2.39.3-9ubuntu2_armhf.deb ...
300s Unpacking eject (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
300s Preparing to unpack .../10-libbpf1_1%3a1.3.0-2build1_armhf.deb ...
300s Unpacking libbpf1:armhf (1:1.3.0-2build1) over (1:1.3.0-2) ...
301s Preparing to unpack .../11-iproute2_6.1.0-1ubuntu5_armhf.deb ...
301s Unpacking iproute2 (6.1.0-1ubuntu5) over (6.1.0-1ubuntu2) ...
301s (Reading database ... 
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301s Removing libelf1:armhf (0.190-1) ...
301s Selecting previously unselected package libelf1t64:armhf.
301s (Reading database ... 
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301s Preparing to unpack .../libelf1t64_0.190-1.1build2_armhf.deb ...
301s Unpacking libelf1t64:armhf (0.190-1.1build2) ...
301s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ...
301s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
301s Preparing to unpack .../lsof_4.95.0-1build2_armhf.deb ...
301s Unpacking lsof (4.95.0-1build2) over (4.95.0-1build1) ...
302s Preparing to unpack .../libnsl2_1.3.0-3build2_armhf.deb ...
302s Unpacking libnsl2:armhf (1.3.0-3build2) over (1.3.0-3) ...
302s (Reading database ... 
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302s Removing libtirpc3:armhf (1.3.4+ds-1build1) ...
302s (Reading database ... 
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302s Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-5.1ubuntu1_armhf.deb ...
302s Unpacking libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ...
302s Preparing to unpack .../1-libkrb5-3_1.20.1-5.1ubuntu1_armhf.deb ...
302s Unpacking libkrb5-3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ...
302s Preparing to unpack .../2-libkrb5support0_1.20.1-5.1ubuntu1_armhf.deb ...
302s Unpacking libkrb5support0:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ...
302s Preparing to unpack .../3-libk5crypto3_1.20.1-5.1ubuntu1_armhf.deb ...
302s Unpacking libk5crypto3:armhf (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ...
302s Preparing to unpack .../4-libcom-err2_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
302s Unpacking libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
302s Selecting previously unselected package libtirpc3t64:armhf.
302s Preparing to unpack .../5-libtirpc3t64_1.3.4+ds-1.1_armhf.deb ...
302s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64'
302s Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
302s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1) ...
303s Preparing to unpack .../6-libc-bin_2.39-0ubuntu6_armhf.deb ...
303s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
303s Setting up libc-bin (2.39-0ubuntu6) ...
303s (Reading database ... 
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303s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ...
303s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ...
304s Preparing to unpack .../vim-tiny_2%3a9.1.0016-1ubuntu5_armhf.deb ...
304s Unpacking vim-tiny (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ...
304s Preparing to unpack .../vim-common_2%3a9.1.0016-1ubuntu5_all.deb ...
304s Unpacking vim-common (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ...
305s Preparing to unpack .../e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ...
305s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
305s Preparing to unpack .../libblockdev-fs3_3.1.0-1build1_armhf.deb ...
305s Unpacking libblockdev-fs3:armhf (3.1.0-1build1) over (3.1.0-1) ...
305s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested:
305s  btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27).
305s 
305s (Reading database ... 
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305s Removing libreiserfscore0 (1:3.6.27-7) ...
305s Selecting previously unselected package libreiserfscore0t64.
305s (Reading database ... 
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305s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_armhf.deb ...
305s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ...
305s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_armhf.deb ...
305s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ...
305s dpkg: libext2fs2:armhf: dependency problems, but removing anyway as you requested:
305s  e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1).
305s 
306s (Reading database ... 
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306s Removing libext2fs2:armhf (1.47.0-2ubuntu1) ...
306s Selecting previously unselected package libext2fs2t64:armhf.
306s (Reading database ... 
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306s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
306s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64'
306s Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
306s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64'
306s Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
306s Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ...
306s Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu2) ...
306s Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu2) ...
306s (Reading database ... 
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306s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
306s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
306s Preparing to unpack .../libblockdev-loop3_3.1.0-1build1_armhf.deb ...
306s Unpacking libblockdev-loop3:armhf (3.1.0-1build1) over (3.1.0-1) ...
306s Preparing to unpack .../libblockdev-mdraid3_3.1.0-1build1_armhf.deb ...
306s Unpacking libblockdev-mdraid3:armhf (3.1.0-1build1) over (3.1.0-1) ...
306s Preparing to unpack .../libblockdev-nvme3_3.1.0-1build1_armhf.deb ...
306s Unpacking libblockdev-nvme3:armhf (3.1.0-1build1) over (3.1.0-1) ...
307s (Reading database ... 
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307s Removing libnvme1 (1.8-2) ...
307s Selecting previously unselected package libnvme1t64.
307s (Reading database ... 
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307s Preparing to unpack .../00-libnvme1t64_1.8-3_armhf.deb ...
307s Unpacking libnvme1t64 (1.8-3) ...
307s Preparing to unpack .../01-libblockdev-part3_3.1.0-1build1_armhf.deb ...
307s Unpacking libblockdev-part3:armhf (3.1.0-1build1) over (3.1.0-1) ...
307s Preparing to unpack .../02-libblockdev-swap3_3.1.0-1build1_armhf.deb ...
307s Unpacking libblockdev-swap3:armhf (3.1.0-1build1) over (3.1.0-1) ...
307s Preparing to unpack .../03-libblockdev3_3.1.0-1build1_armhf.deb ...
307s Unpacking libblockdev3:armhf (3.1.0-1build1) over (3.1.0-1) ...
307s Preparing to unpack .../04-libgudev-1.0-0_1%3a238-3ubuntu2_armhf.deb ...
307s Unpacking libgudev-1.0-0:armhf (1:238-3ubuntu2) over (1:238-3) ...
307s Preparing to unpack .../05-libxml2_2.9.14+dfsg-1.3ubuntu2_armhf.deb ...
307s Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) over (2.9.14+dfsg-1.3ubuntu1) ...
307s Preparing to unpack .../06-libmbim-proxy_1.31.2-0ubuntu2_armhf.deb ...
307s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ...
308s Preparing to unpack .../07-libmbim-glib4_1.31.2-0ubuntu2_armhf.deb ...
308s Unpacking libmbim-glib4:armhf (1.31.2-0ubuntu2) over (1.30.0-1) ...
308s Preparing to unpack .../08-libjson-glib-1.0-common_1.8.0-2build1_all.deb ...
308s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ...
308s Preparing to unpack .../09-libjson-glib-1.0-0_1.8.0-2build1_armhf.deb ...
308s Unpacking libjson-glib-1.0-0:armhf (1.8.0-2build1) over (1.8.0-2) ...
308s Preparing to unpack .../10-libusb-1.0-0_2%3a1.0.27-1_armhf.deb ...
308s Unpacking libusb-1.0-0:armhf (2:1.0.27-1) over (2:1.0.26-1) ...
308s Preparing to unpack .../11-libgusb2_0.4.8-1build1_armhf.deb ...
308s Unpacking libgusb2:armhf (0.4.8-1build1) over (0.4.8-1) ...
308s Preparing to unpack .../12-libmm-glib0_1.23.4-0ubuntu1_armhf.deb ...
308s Unpacking libmm-glib0:armhf (1.23.4-0ubuntu1) over (1.22.0-3) ...
308s Preparing to unpack .../13-libprotobuf-c1_1.4.1-1ubuntu3_armhf.deb ...
308s Unpacking libprotobuf-c1:armhf (1.4.1-1ubuntu3) over (1.4.1-1ubuntu2) ...
308s Preparing to unpack .../14-libbrotli1_1.1.0-2build1_armhf.deb ...
308s Unpacking libbrotli1:armhf (1.1.0-2build1) over (1.1.0-2) ...
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309s Preparing to unpack .../18-libfido2-1_1.14.0-1build1_armhf.deb ...
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309s Preparing to unpack .../19-coreutils_9.4-3ubuntu3_armhf.deb ...
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309s Setting up coreutils (9.4-3ubuntu3) ...
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309s Preparing to unpack .../debianutils_5.17_armhf.deb ...
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310s Preparing to unpack .../util-linux_2.39.3-9ubuntu2_armhf.deb ...
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310s Setting up util-linux (2.39.3-9ubuntu2) ...
312s fstrim.service is a disabled or a static unit not running, not starting it.
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312s Removing libatm1:armhf (1:2.5.1-5) ...
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313s Preparing to unpack .../curl_8.5.0-2ubuntu7_armhf.deb ...
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313s Removing libcurl4:armhf (8.5.0-2ubuntu2) ...
313s Selecting previously unselected package libcurl4t64:armhf.
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313s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_armhf.deb ...
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313s Preparing to unpack .../file_1%3a5.45-3_armhf.deb ...
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313s Removing libmagic1:armhf (1:5.45-2) ...
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314s Preparing to unpack .../libmagic-mgc_1%3a5.45-3_armhf.deb ...
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314s Selecting previously unselected package libmagic1t64:armhf.
314s Preparing to unpack .../libmagic1t64_1%3a5.45-3_armhf.deb ...
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314s Preparing to unpack .../libplymouth5_24.004.60-1ubuntu6_armhf.deb ...
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314s Removing libpng16-16:armhf (1.6.43-1) ...
314s Selecting previously unselected package libpng16-16t64:armhf.
314s (Reading database ... 
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314s Preparing to unpack .../libpng16-16t64_1.6.43-3_armhf.deb ...
314s Unpacking libpng16-16t64:armhf (1.6.43-3) ...
314s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_armhf.deb ...
314s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
314s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_armhf.deb ...
314s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
315s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_armhf.deb ...
315s Unpacking bind9-libs:armhf (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
315s (Reading database ... 
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315s Removing libuv1:armhf (1.48.0-1) ...
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315s (Reading database ... 
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315s Preparing to unpack .../libuv1t64_1.48.0-1.1_armhf.deb ...
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315s Removing python3-distutils (3.11.5-1) ...
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316s Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu2_armhf.deb ...
316s Unpacking uuid-runtime (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
316s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_armhf.deb ...
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316s Setting up libdebconfclient0:armhf (0.271ubuntu2) ...
316s (Reading database ... 
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316s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ...
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316s Setting up libsemanage-common (3.5-1build4) ...
316s (Reading database ... 
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316s Preparing to unpack .../libsemanage2_3.5-1build4_armhf.deb ...
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316s Setting up libsemanage2:armhf (3.5-1build4) ...
317s (Reading database ... 
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317s Preparing to unpack .../install-info_7.1-3build1_armhf.deb ...
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317s Setting up install-info (7.1-3build1) ...
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317s Preparing to unpack .../00-gcc-13-base_13.2.0-19ubuntu1_armhf.deb ...
317s Unpacking gcc-13-base:armhf (13.2.0-19ubuntu1) over (13.2.0-17ubuntu2) ...
317s Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu2_armhf.deb ...
317s Unpacking libss2:armhf (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
317s Preparing to unpack .../02-dmsetup_2%3a1.02.185-3ubuntu2_armhf.deb ...
317s Unpacking dmsetup (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ...
317s Preparing to unpack .../03-krb5-locales_1.20.1-5.1ubuntu1_all.deb ...
317s Unpacking krb5-locales (1.20.1-5.1ubuntu1) over (1.20.1-5build1) ...
317s Preparing to unpack .../04-libbsd0_0.12.1-1_armhf.deb ...
317s Unpacking libbsd0:armhf (0.12.1-1) over (0.11.8-1) ...
318s Preparing to unpack .../05-libglib2.0-data_2.79.3-3ubuntu5_all.deb ...
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318s Preparing to unpack .../06-libslang2_2.3.3-3build1_armhf.deb ...
318s Unpacking libslang2:armhf (2.3.3-3build1) over (2.3.3-3) ...
318s Selecting previously unselected package xdg-user-dirs.
318s Preparing to unpack .../07-xdg-user-dirs_0.18-1_armhf.deb ...
318s Unpacking xdg-user-dirs (0.18-1) ...
318s Preparing to unpack .../08-xxd_2%3a9.1.0016-1ubuntu5_armhf.deb ...
318s Unpacking xxd (2:9.1.0016-1ubuntu5) over (2:9.1.0016-1ubuntu2) ...
318s Preparing to unpack .../09-apparmor_4.0.0-beta3-0ubuntu2_armhf.deb ...
320s Unpacking apparmor (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ...
321s Preparing to unpack .../10-ftp_20230507-2build1_all.deb ...
321s Unpacking ftp (20230507-2build1) over (20230507-2) ...
321s Preparing to unpack .../11-inetutils-telnet_2%3a2.5-3ubuntu3_armhf.deb ...
321s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ...
321s Preparing to unpack .../12-info_7.1-3build1_armhf.deb ...
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321s Preparing to unpack .../13-libxmuu1_2%3a1.1.3-3build1_armhf.deb ...
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321s Preparing to unpack .../14-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_armhf.deb ...
321s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ...
321s Preparing to unpack .../15-mtr-tiny_0.95-1.1build1_armhf.deb ...
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321s Preparing to unpack .../16-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_armhf.deb ...
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322s Preparing to unpack .../17-plymouth_24.004.60-1ubuntu6_armhf.deb ...
322s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ...
322s Preparing to unpack .../18-psmisc_23.7-1_armhf.deb ...
322s Unpacking psmisc (23.7-1) over (23.6-2) ...
322s Preparing to unpack .../19-telnet_0.17+2.5-3ubuntu3_all.deb ...
322s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ...
322s Preparing to unpack .../20-xz-utils_5.6.0-0.2_armhf.deb ...
322s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ...
323s Preparing to unpack .../21-ubuntu-standard_1.536build1_armhf.deb ...
323s Unpacking ubuntu-standard (1.536build1) over (1.536) ...
323s Preparing to unpack .../22-usb.ids_2024.03.18-1_all.deb ...
323s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ...
323s Preparing to unpack .../23-libctf-nobfd0_2.42-4ubuntu1_armhf.deb ...
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323s Preparing to unpack .../24-libctf0_2.42-4ubuntu1_armhf.deb ...
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323s Preparing to unpack .../25-binutils-arm-linux-gnueabihf_2.42-4ubuntu1_armhf.deb ...
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323s Preparing to unpack .../26-libbinutils_2.42-4ubuntu1_armhf.deb ...
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323s Preparing to unpack .../27-binutils_2.42-4ubuntu1_armhf.deb ...
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323s Preparing to unpack .../28-binutils-common_2.42-4ubuntu1_armhf.deb ...
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324s Preparing to unpack .../29-libsframe1_2.42-4ubuntu1_armhf.deb ...
324s Unpacking libsframe1:armhf (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
324s Preparing to unpack .../30-bolt_0.9.6-2build1_armhf.deb ...
324s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ...
324s Preparing to unpack .../31-cryptsetup-bin_2%3a2.7.0-1ubuntu2_armhf.deb ...
324s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
324s Preparing to unpack .../32-dpkg-dev_1.22.6ubuntu4_all.deb ...
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324s Preparing to unpack .../33-libdpkg-perl_1.22.6ubuntu4_all.deb ...
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325s Preparing to unpack .../34-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ...
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325s Preparing to unpack .../35-gnupg-l10n_2.4.4-2ubuntu15_all.deb ...
325s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
325s Preparing to unpack .../36-ibverbs-providers_50.0-2build1_armhf.deb ...
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325s Preparing to unpack .../37-jq_1.7.1-3_armhf.deb ...
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325s Selecting previously unselected package libatm1t64:armhf.
325s Preparing to unpack .../39-libatm1t64_1%3a2.5.1-5.1_armhf.deb ...
325s Unpacking libatm1t64:armhf (1:2.5.1-5.1) ...
326s Preparing to unpack .../40-libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ...
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326s Preparing to unpack .../41-libftdi1-2_1.5-6build4_armhf.deb ...
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326s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
326s Preparing to unpack .../43-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_armhf.deb ...
326s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
326s Preparing to unpack .../44-python3-lib2to3_3.12.2-3ubuntu2_all.deb ...
326s Unpacking python3-lib2to3 (3.12.2-3ubuntu2) over (3.11.5-1) ...
326s Preparing to unpack .../45-python3-markupsafe_2.1.5-1build1_armhf.deb ...
327s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ...
327s Preparing to unpack .../46-python3-pyrsistent_0.20.0-1build1_armhf.deb ...
327s Unpacking python3-pyrsistent:armhf (0.20.0-1build1) over (0.20.0-1) ...
327s Preparing to unpack .../47-python3-typing-extensions_4.10.0-1_all.deb ...
327s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ...
328s Preparing to unpack .../48-cloud-init_24.1.2-0ubuntu1_all.deb ...
328s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ...
329s Preparing to unpack .../49-kpartx_0.9.4-5ubuntu6_armhf.deb ...
329s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ...
329s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ...
329s Setting up pinentry-curses (1.2.1-3ubuntu4) ...
329s Setting up libtext-iconv-perl:armhf (1.7-8build2) ...
329s Setting up libtext-charwidth-perl:armhf (0.04-11build2) ...
329s Setting up libibverbs1:armhf (50.0-2build1) ...
329s Setting up systemd-sysv (255.4-1ubuntu5) ...
329s Setting up libapparmor1:armhf (4.0.0-beta3-0ubuntu2) ...
329s Setting up libatm1t64:armhf (1:2.5.1-5.1) ...
329s Setting up libgdbm6t64:armhf (1.23-5.1) ...
329s Setting up bsdextrautils (2.39.3-9ubuntu2) ...
329s Setting up libgdbm-compat4t64:armhf (1.23-5.1) ...
329s Setting up xdg-user-dirs (0.18-1) ...
329s Setting up ibverbs-providers:armhf (50.0-2build1) ...
329s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ...
329s Setting up libmagic-mgc (1:5.45-3) ...
329s Setting up gawk (1:5.2.1-2build2) ...
329s Setting up psmisc (23.7-1) ...
329s Setting up libjq1:armhf (1.7.1-3) ...
329s Setting up libtirpc-common (1.3.4+ds-1.1) ...
329s Setting up libbrotli1:armhf (1.1.0-2build1) ...
329s Setting up libsqlite3-0:armhf (3.45.1-1ubuntu1) ...
329s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-5ubuntu1) ...
329s Setting up libuv1t64:armhf (1.48.0-1.1) ...
329s Setting up libmagic1t64:armhf (1:5.45-3) ...
329s Setting up binutils-common:armhf (2.42-4ubuntu1) ...
329s Setting up libpsl5t64:armhf (0.21.2-1.1) ...
329s Setting up libnghttp2-14:armhf (1.59.0-1build1) ...
329s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ...
329s Setting up libctf-nobfd0:armhf (2.42-4ubuntu1) ...
329s Setting up libnss-systemd:armhf (255.4-1ubuntu5) ...
329s Setting up krb5-locales (1.20.1-5.1ubuntu1) ...
329s Setting up file (1:5.45-3) ...
329s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ...
329s Setting up locales (2.39-0ubuntu6) ...
331s Generating locales (this might take a while)...
339s   en_US.UTF-8... done
339s Generation complete.
339s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ...
339s Setting up libprotobuf-c1:armhf (1.4.1-1ubuntu3) ...
339s Setting up xxd (2:9.1.0016-1ubuntu5) ...
339s Setting up libsframe1:armhf (2.42-4ubuntu1) ...
339s Setting up libelf1t64:armhf (0.190-1.1build2) ...
339s Setting up libkrb5support0:armhf (1.20.1-5.1ubuntu1) ...
339s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ...
339s Setting up eject (2.39.3-9ubuntu2) ...
339s Setting up apparmor (4.0.0-beta3-0ubuntu2) ...
339s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
339s Installing new version of config file /etc/apparmor.d/abstractions/crypto ...
339s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ...
339s Installing new version of config file /etc/apparmor.d/abstractions/openssl ...
340s Installing new version of config file /etc/apparmor.d/code ...
340s Installing new version of config file /etc/apparmor.d/firefox ...
340s apparmor_parser: Unable to replace "lsb_release".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
340s 
340s apparmor_parser: Unable to replace "kmod".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
340s 
340s apparmor_parser: Unable to replace "nvidia_modprobe".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
340s 
343s sysctl: cannot stat /proc/sys/kernel/apparmor_restrict_unprivileged_userns: No such file or directory
343s Reloading AppArmor profiles 
343s /sbin/apparmor_parser: Unable to replace "1password".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "Discord".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "MongoDB Compass".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "brave".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "busybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "buildah".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "cam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "ch-checkns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "ch-run".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "chrome".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "vscode".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "crun".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "element-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "devhelp".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "evolution".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "firefox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "epiphany".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "flatpak".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "goldendict".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "geary".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "github-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "ipa_verify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "keybase".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "kchmviewer".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "libcamerify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "linux-sandbox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lc-compliance".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lxc-attach".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lxc-create".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "loupe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lxc-destroy".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lxc-execute".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lxc-stop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "lxc-unshare".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "mmdebstrap".  /sbin/apparmor_parser: Unable to replace "lxc-usernsexec".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "msedge".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "nautilus".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "notepadqq".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "obsidian".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "opam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "podman".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "polypane".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "qcam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "privacybrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "opera".  /sbin/apparmor_parser: Unable to replace "qmapshack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "qutebrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "pageedit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "rootlesskit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "runc".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "rssguard".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "rpm".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-apt".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-abort".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-hold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-adduser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-unhold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "plasmashell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-update".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-clean".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade".  /sbin/apparmor_parser: Unable to replace "slack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "signal-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "sbuild-shell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "slirp4netns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "scide".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "stress-ng".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "steam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "trinity".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "surfshark".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "tup".  /sbin/apparmor_parser: Unable to replace "toybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "thunderbird".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "systemd-coredump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "userbindmount".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
343s /sbin/apparmor_parser: Unable to replace "unprivileged_userns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
343s 
344s /sbin/apparmor_parser: Unable to replace "uwsgi-core".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "vdens".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "virtiofsd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "vivaldi-bin".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "lsb_release".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "vpnns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "wpcom".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "kmod".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "rsyslogd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "unix-chkpwd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "/usr/bin/man".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s /sbin/apparmor_parser: Unable to replace "tcpdump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
344s 
344s Error: At least one profile failed to load
344s Setting up libglib2.0-0t64:armhf (2.79.3-3ubuntu5) ...
344s No schema files found: doing nothing.
344s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
344s Setting up vim-common (2:9.1.0016-1ubuntu5) ...
344s Setting up gcc-13-base:armhf (13.2.0-19ubuntu1) ...
344s Setting up libqrtr-glib0:armhf (1.2.2-1ubuntu3) ...
344s Setting up libslang2:armhf (2.3.3-3build1) ...
344s Setting up libnvme1t64 (1.8-3) ...
344s Setting up mtr-tiny (0.95-1.1build1) ...
344s Setting up gnupg-l10n (2.4.4-2ubuntu15) ...
344s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build6) ...
344s Setting up libdbus-1-3:armhf (1.14.10-4ubuntu2) ...
344s Setting up xz-utils (5.6.0-0.2) ...
344s Setting up perl-modules-5.38 (5.38.2-3.2) ...
344s Setting up libpng16-16t64:armhf (1.6.43-3) ...
344s Setting up systemd-timesyncd (255.4-1ubuntu5) ...
346s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ...
346s Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu2) ...
346s Setting up usb.ids (2024.03.18-1) ...
346s Setting up sudo (1.9.15p5-3ubuntu3) ...
346s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ...
346s Setting up gir1.2-glib-2.0:armhf (2.79.3-3ubuntu5) ...
346s Setting up libk5crypto3:armhf (1.20.1-5.1ubuntu1) ...
346s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ...
346s Setting up libfdisk1:armhf (2.39.3-9ubuntu2) ...
346s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-6) ...
346s Setting up libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu2) ...
346s Setting up python-apt-common (2.7.6build1) ...
346s Setting up mount (2.39.3-9ubuntu2) ...
346s Setting up dmsetup (2:1.02.185-3ubuntu2) ...
346s Setting up uuid-runtime (2.39.3-9ubuntu2) ...
349s uuidd.service is a disabled or a static unit not running, not starting it.
349s Setting up libmm-glib0:armhf (1.23.4-0ubuntu1) ...
349s Setting up groff-base (1.23.0-3build1) ...
349s Setting up libplymouth5:armhf (24.004.60-1ubuntu6) ...
349s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ...
349s Setting up jq (1.7.1-3) ...
349s Setting up gpgconf (2.4.4-2ubuntu15) ...
349s Setting up libpcap0.8t64:armhf (1.10.4-4.1ubuntu1) ...
349s Setting up libcryptsetup12:armhf (2:2.7.0-1ubuntu2) ...
349s Setting up libgirepository-1.0-1:armhf (1.79.1-1ubuntu6) ...
349s Setting up libjson-glib-1.0-common (1.8.0-2build1) ...
349s Setting up libkrb5-3:armhf (1.20.1-5.1ubuntu1) ...
349s Setting up libpython3.11-minimal:armhf (3.11.8-1build4) ...
349s Setting up libusb-1.0-0:armhf (2:1.0.27-1) ...
349s Setting up libperl5.38t64:armhf (5.38.2-3.2) ...
350s Setting up tnftp (20230507-2build1) ...
350s Setting up libbinutils:armhf (2.42-4ubuntu1) ...
350s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ...
350s Setting up libfido2-1:armhf (1.14.0-1build1) ...
350s Setting up openssl (3.0.13-0ubuntu2) ...
350s Setting up libbsd0:armhf (0.12.1-1) ...
350s Setting up readline-common (8.2-3.1build1) ...
350s Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu2) ...
350s Setting up libxmuu1:armhf (2:1.1.3-3build1) ...
350s Setting up dbus-bin (1.14.10-4ubuntu2) ...
350s Setting up info (7.1-3build1) ...
350s Setting up liblocale-gettext-perl (1.07-6ubuntu3) ...
350s Setting up gpg (2.4.4-2ubuntu15) ...
350s Setting up libgudev-1.0-0:armhf (1:238-3ubuntu2) ...
350s Setting up libpolkit-gobject-1-0:armhf (124-1ubuntu1) ...
350s Setting up libbpf1:armhf (1:1.3.0-2build1) ...
350s Setting up libmbim-glib4:armhf (1.31.2-0ubuntu2) ...
350s Setting up rsync (3.2.7-1build1) ...
353s rsync.service is a disabled or a static unit not running, not starting it.
353s Setting up libudisks2-0:armhf (2.10.1-6) ...
353s Setting up libkmod2:armhf (31+20240202-2ubuntu4) ...
353s Setting up bolt (0.9.6-2build1) ...
354s bolt.service is a disabled or a static unit not running, not starting it.
354s Setting up gnupg-utils (2.4.4-2ubuntu15) ...
354s Setting up initramfs-tools-bin (0.142ubuntu23) ...
354s Setting up libctf0:armhf (2.42-4ubuntu1) ...
354s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ...
354s Setting up python3.11-minimal (3.11.8-1build4) ...
357s Setting up tcpdump (4.99.4-3ubuntu2) ...
358s apparmor_parser: Unable to replace "tcpdump".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
358s 
358s Setting up apt-utils (2.7.13ubuntu1) ...
358s Setting up gpg-agent (2.4.4-2ubuntu15) ...
360s Setting up libpython3.12-stdlib:armhf (3.12.2-4build3) ...
360s Setting up wget (1.21.4-1ubuntu2) ...
360s Setting up libxmlb2:armhf (0.3.15-1build1) ...
360s Setting up btrfs-progs (6.6.3-1.1build1) ...
360s Setting up libpython3.11-stdlib:armhf (3.11.8-1build4) ...
360s Setting up python3.12 (3.12.2-4build3) ...
364s Setting up gpgsm (2.4.4-2ubuntu15) ...
364s Setting up inetutils-telnet (2:2.5-3ubuntu3) ...
364s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ...
364s update-initramfs: deferring update (trigger activated)
366s e2scrub_all.service is a disabled or a static unit not running, not starting it.
366s Setting up libparted2t64:armhf (3.6-3.1build2) ...
366s Setting up linux-headers-generic (6.8.0-20.20+1) ...
366s Setting up dbus-daemon (1.14.10-4ubuntu2) ...
366s Setting up libmbim-proxy (1.31.2-0ubuntu2) ...
366s Setting up vim-tiny (2:9.1.0016-1ubuntu5) ...
366s Setting up kmod (31+20240202-2ubuntu4) ...
367s Setting up libnetplan1:armhf (1.0-1) ...
367s Setting up man-db (2.12.0-3build4) ...
367s Updating database of manual pages ...
371s apparmor_parser: Unable to replace "/usr/bin/man".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
371s 
372s man-db.service is a disabled or a static unit not running, not starting it.
372s Setting up fdisk (2.39.3-9ubuntu2) ...
372s Setting up libjson-glib-1.0-0:armhf (1.8.0-2build1) ...
372s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu1) ...
372s Setting up libftdi1-2:armhf (1.5-6build4) ...
372s Setting up perl (5.38.2-3.2) ...
372s Setting up gir1.2-girepository-2.0:armhf (1.79.1-1ubuntu6) ...
372s Setting up dbus (1.14.10-4ubuntu2) ...
372s A reboot is required to replace the running dbus-daemon.
372s Please reboot the system when convenient.
373s Setting up shared-mime-info (2.4-1build1) ...
375s Setting up libblockdev-utils3:armhf (3.1.0-1build1) ...
375s Setting up libgssapi-krb5-2:armhf (1.20.1-5.1ubuntu1) ...
375s Setting up udev (255.4-1ubuntu5) ...
377s Setting up ftp (20230507-2build1) ...
377s Setting up keyboxd (2.4.4-2ubuntu15) ...
378s Setting up libdpkg-perl (1.22.6ubuntu4) ...
378s Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu1) ...
378s Setting up libssh-4:armhf (0.10.6-2build1) ...
378s Setting up libblockdev-nvme3:armhf (3.1.0-1build1) ...
378s Setting up libblockdev-fs3:armhf (3.1.0-1build1) ...
378s Setting up kpartx (0.9.4-5ubuntu6) ...
378s Setting up libpam-systemd:armhf (255.4-1ubuntu5) ...
379s Setting up libpolkit-agent-1-0:armhf (124-1ubuntu1) ...
379s Setting up libgpgme11t64:armhf (1.18.0-4.1ubuntu3) ...
379s Setting up netplan-generator (1.0-1) ...
379s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
379s Setting up initramfs-tools-core (0.142ubuntu23) ...
379s Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu1) ...
379s Setting up libarchive13t64:armhf (3.7.2-1.1ubuntu2) ...
379s Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ...
379s Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu1) ...
379s Setting up systemd-resolved (255.4-1ubuntu5) ...
381s Setting up python3.11 (3.11.8-1build4) ...
384s Setting up telnet (0.17+2.5-3ubuntu3) ...
384s Setting up initramfs-tools (0.142ubuntu23) ...
384s update-initramfs: deferring update (trigger activated)
384s Setting up libblockdev-mdraid3:armhf (3.1.0-1build1) ...
384s Setting up libcurl4t64:armhf (8.5.0-2ubuntu7) ...
384s Setting up bind9-libs:armhf (1:9.18.24-0ubuntu3) ...
384s Setting up libtirpc3t64:armhf (1.3.4+ds-1.1) ...
384s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ...
384s Setting up libblockdev-swap3:armhf (3.1.0-1build1) ...
384s Setting up plymouth (24.004.60-1ubuntu6) ...
385s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
385s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
386s Setting up iproute2 (6.1.0-1ubuntu5) ...
386s Setting up openssh-client (1:9.6p1-3ubuntu11) ...
386s Setting up libgusb2:armhf (0.4.8-1build1) ...
386s Setting up libblockdev-loop3:armhf (3.1.0-1build1) ...
386s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu7) ...
386s Setting up parted (3.6-3.1build2) ...
386s Setting up libqmi-glib5:armhf (1.35.2-0ubuntu1) ...
386s Setting up python3 (3.12.2-0ubuntu1) ...
387s Setting up binutils (2.42-4ubuntu1) ...
387s Setting up python3-markupsafe (2.1.5-1build1) ...
388s Setting up libblockdev3:armhf (3.1.0-1build1) ...
388s Setting up libjcat1:armhf (0.2.0-2build2) ...
388s Setting up dpkg-dev (1.22.6ubuntu4) ...
388s Setting up libblockdev-part3:armhf (3.1.0-1build1) ...
388s Setting up dirmngr (2.4.4-2ubuntu15) ...
388s Setting up dbus-user-session (1.14.10-4ubuntu2) ...
388s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ...
388s update-initramfs: deferring update (trigger activated)
388s Setting up python3-cryptography (41.0.7-4build2) ...
389s Setting up python3-gi (3.47.0-3build1) ...
390s Setting up python3-typing-extensions (4.10.0-1) ...
390s Setting up lsof (4.95.0-1build2) ...
390s Setting up python3-pyrsistent:armhf (0.20.0-1build1) ...
391s Setting up libnsl2:armhf (1.3.0-3build2) ...
391s Setting up gnupg (2.4.4-2ubuntu15) ...
391s Setting up python3-netplan (1.0-1) ...
391s Setting up curl (8.5.0-2ubuntu7) ...
391s Setting up libvolume-key1:armhf (0.3.12-7build1) ...
391s Setting up bind9-host (1:9.18.24-0ubuntu3) ...
391s Setting up python3-lib2to3 (3.12.2-3ubuntu2) ...
392s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ...
393s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ...
393s Setting up python3-dbus (1.3.2-5build2) ...
393s Setting up python3-setuptools (68.1.2-2ubuntu1) ...
395s Setting up gpg-wks-client (2.4.4-2ubuntu15) ...
395s Setting up openssh-server (1:9.6p1-3ubuntu11) ...
396s Replacing config file /etc/ssh/sshd_config with new version
400s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket.

403s Setting up libblockdev-crypto3:armhf (3.1.0-1build1) ...
403s Setting up python3-gdbm:armhf (3.12.2-3ubuntu2) ...
403s Setting up python3-apt (2.7.6build1) ...
404s Setting up libfwupd2:armhf (1.9.15-1) ...
404s Setting up python3-yaml (6.0.1-2build1) ...
405s Setting up libqmi-proxy (1.35.2-0ubuntu1) ...
405s Setting up netplan.io (1.0-1) ...
405s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ...
405s Setting up ubuntu-pro-client (31.2.1) ...
405s apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
405s 
410s Setting up fwupd (1.9.15-1) ...
411s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
411s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
411s fwupd.service is a disabled or a static unit not running, not starting it.
411s Setting up ubuntu-pro-client-l10n (31.2.1) ...
411s Setting up udisks2 (2.10.1-6) ...
412s sda: Failed to write 'change' to '/sys/devices/platform/a003e00.virtio_mmio/virtio2/host0/target0:0:0/0:0:0:0/block/sda/uevent': Permission denied

412s sda1: Failed to write 'change' to '/sys/devices/platform/a003e00.virtio_mmio/virtio2/host0/target0:0:0/0:0:0:0/block/sda/sda1/uevent': Permission denied

412s sda15: Failed to write 'change' to '/sys/devices/platform/a003e00.virtio_mmio/virtio2/host0/target0:0:0/0:0:0:0/block/sda/sda15/uevent': Permission denied

412s sda2: Failed to write 'change' to '/sys/devices/platform/a003e00.virtio_mmio/virtio2/host0/target0:0:0/0:0:0:0/block/sda/sda2/uevent': Permission denied

412s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied

412s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied

412s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied

412s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied

412s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied

412s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied

412s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied

412s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied

413s Setting up cloud-init (24.1.2-0ubuntu1) ...
418s Setting up ubuntu-minimal (1.536build1) ...
418s Setting up ubuntu-standard (1.536build1) ...
418s Processing triggers for libc-bin (2.39-0ubuntu6) ...
419s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
419s Processing triggers for ufw (0.36.2-5) ...
419s Processing triggers for install-info (7.1-3build1) ...
419s Processing triggers for initramfs-tools (0.142ubuntu23) ...
425s Reading package lists...
426s Building dependency tree...
426s Reading state information...
429s The following packages will be REMOVED:
429s   linux-headers-6.8.0-11* python3-lib2to3*
430s 0 upgraded, 0 newly installed, 2 to remove and 1 not upgraded.
430s After this operation, 85.8 MB disk space will be freed.
430s (Reading database ... 
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(Reading database ... 78592 files and directories currently installed.)
430s Removing linux-headers-6.8.0-11 (6.8.0-11.11) ...
434s Removing python3-lib2to3 (3.12.2-3ubuntu2) ...
438s autopkgtest [19:18:43]: rebooting testbed after setup commands that affected boot
495s autopkgtest [19:19:40]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024
528s autopkgtest [19:20:13]: @@@@@@@@@@@@@@@@@@@@ apt-source bcftools
545s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe bcftools 1.19-1build1 (dsc) [2260 B]
545s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe bcftools 1.19-1build1 (tar) [3540 kB]
545s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe bcftools 1.19-1build1 (diff) [11.2 kB]
545s gpgv: Signature made Fri Mar 22 15:49:59 2024 UTC
545s gpgv:                using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71
545s gpgv:                issuer "juliank@ubuntu.com"
545s gpgv: Can't check signature: No public key
545s dpkg-source: warning: cannot verify inline signature for ./bcftools_1.19-1build1.dsc: no acceptable signature found
546s autopkgtest [19:20:31]: testing package bcftools version 1.19-1build1
549s autopkgtest [19:20:34]: build not needed
559s autopkgtest [19:20:44]: test command1: preparing testbed
572s Reading package lists...
573s Building dependency tree...
573s Reading state information...
574s Starting pkgProblemResolver with broken count: 0
575s Starting 2 pkgProblemResolver with broken count: 0
575s Done
576s The following additional packages will be installed:
577s   bcftools libdeflate0 libhts3t64 libhtscodecs2 tabix
577s Suggested packages:
577s   python3-numpy python3-matplotlib texlive-latex-recommended
577s The following NEW packages will be installed:
577s   autopkgtest-satdep bcftools libdeflate0 libhts3t64 libhtscodecs2 tabix
577s 0 upgraded, 6 newly installed, 0 to remove and 1 not upgraded.
577s Need to get 1627 kB/1628 kB of archives.
577s After this operation, 4202 kB of additional disk space will be used.
577s Get:1 /tmp/autopkgtest.M9R37K/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B]
577s Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB]
577s Get:3 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB]
577s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libhts3t64 armhf 1.19+ds-1.1build2 [389 kB]
578s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf bcftools armhf 1.19-1build1 [703 kB]
578s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tabix armhf 1.19+ds-1.1build2 [428 kB]
579s Fetched 1627 kB in 1s (1560 kB/s)
579s Selecting previously unselected package libdeflate0:armhf.
579s (Reading database ... 
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(Reading database ... 58435 files and directories currently installed.)
579s Preparing to unpack .../0-libdeflate0_1.19-1_armhf.deb ...
579s Unpacking libdeflate0:armhf (1.19-1) ...
579s Selecting previously unselected package libhtscodecs2:armhf.
580s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_armhf.deb ...
580s Unpacking libhtscodecs2:armhf (1.6.0-1) ...
580s Selecting previously unselected package libhts3t64:armhf.
580s Preparing to unpack .../2-libhts3t64_1.19+ds-1.1build2_armhf.deb ...
580s Unpacking libhts3t64:armhf (1.19+ds-1.1build2) ...
580s Selecting previously unselected package bcftools.
580s Preparing to unpack .../3-bcftools_1.19-1build1_armhf.deb ...
580s Unpacking bcftools (1.19-1build1) ...
580s Selecting previously unselected package tabix.
580s Preparing to unpack .../4-tabix_1.19+ds-1.1build2_armhf.deb ...
580s Unpacking tabix (1.19+ds-1.1build2) ...
580s Selecting previously unselected package autopkgtest-satdep.
580s Preparing to unpack .../5-1-autopkgtest-satdep.deb ...
580s Unpacking autopkgtest-satdep (0) ...
580s Setting up libhtscodecs2:armhf (1.6.0-1) ...
580s Setting up libdeflate0:armhf (1.19-1) ...
580s Setting up libhts3t64:armhf (1.19+ds-1.1build2) ...
580s Setting up tabix (1.19+ds-1.1build2) ...
580s Setting up bcftools (1.19-1build1) ...
580s Setting up autopkgtest-satdep (0) ...
580s Processing triggers for man-db (2.12.0-3build4) ...
581s Processing triggers for libc-bin (2.39-0ubuntu6) ...
601s (Reading database ... 58525 files and directories currently installed.)
601s Removing autopkgtest-satdep (0) ...
611s autopkgtest [19:21:36]: test command1: 	mv -f bcftools bcftools.orig || /bin/true; ln -s /usr/bin/bcftools bcftools &&	./test/test.pl	--exec bgzip=/usr/bin/bgzip	--exec tabix=/usr/bin/tabix && mv -f bcftools.orig bcftools || /bin/true
611s autopkgtest [19:21:36]: test command1: [-----------------------
614s mv: cannot stat 'bcftools': No such file or directory
614s ./test/test.pl: module IO::Pty not found; skipping usage tests
614s test_usage:
614s 	bcftools
614s test_tabix:
614s 	/usr/bin/tabix /tmp/vR10W27JBX/merge.a.vcf.gz 2:3199812-3199812
614s .. ok
614s 
614s test_tabix:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/merge.a.bcf 2:3199812-3199812
614s .. ok
614s 
614s test_tabix:
614s 	/usr/bin/tabix /tmp/vR10W27JBX/merge.a.vcf.gz 1:3000151-3000151
614s .. ok
614s 
614s test_tabix:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/merge.a.bcf 1:3000151-3000151
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.bcf chr20:1-2147483647
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.bcf chr20:1-2147483647
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.bcf chr20:1-2147483647
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.vcf.gz chr20
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.bcf chr20
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.bcf chr20
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.vcf.gz chr20
614s .. ok
614s 
614s test_index:
614s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H /tmp/vR10W27JBX/large_chrom_csi_limit.bcf chr20
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -s /tmp/vR10W27JBX/idx.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -s /tmp/vR10W27JBX/idx.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -s /tmp/vR10W27JBX/idx.bcf
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/idx.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/idx.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/idx.vcf.gz.csi
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/idx.bcf
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/idx.bcf.csi
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -s /tmp/vR10W27JBX/empty.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -s /tmp/vR10W27JBX/empty.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -s /tmp/vR10W27JBX/empty.bcf
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/empty.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/empty.vcf.gz
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/empty.vcf.gz.csi
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/empty.bcf
615s .. ok
615s 
615s test_vcf_idxstats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools index -n /tmp/vR10W27JBX/empty.bcf.csi
615s .. ok
615s 
615s test_vcf_check:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s - /tmp/vR10W27JBX/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
615s .. ok
615s 
615s test_vcf_check:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
615s .. ok
615s 
615s test_vcf_check_merge:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/misc/plot-vcfstats -m /tmp/vR10W27JBX/check.1.chk /tmp/vR10W27JBX/check.2.chk /tmp/vR10W27JBX/check.3.chk /tmp/vR10W27JBX/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
615s .. ok
615s 
615s test_vcf_stats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s -  /tmp/vR10W27JBX/stats.a.vcf.gz /tmp/vR10W27JBX/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
615s .. ok
615s 
615s test_vcf_stats:
615s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s B  /tmp/vR10W27JBX/stats.a.vcf.gz /tmp/vR10W27JBX/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
616s .. ok
616s 
616s test_vcf_stats:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s -  /tmp/vR10W27JBX/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
616s .. ok
616s 
616s test_vcf_stats:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s - -i 'type="snp"'  /tmp/vR10W27JBX/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
616s .. ok
616s 
616s test_vcf_stats:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools stats -s -  /tmp/vR10W27JBX/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID	'
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -n =2 /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -n =2 /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -n =2 -c both /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -n =2 -c both /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -n =2 -c any /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -n =2 -c any /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -C -c any /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -C -c any /tmp/vR10W27JBX/isec.a.vcf.gz /tmp/vR10W27JBX/isec.b.vcf.gz
616s .. ok
616s 
616s test_vcf_isec2:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec --no-version   -T /tmp/vR10W27JBX/isec.tab.gz /tmp/vR10W27JBX/isec.a.vcf.gz
616s .. ok
616s 
616s test_vcf_isec2:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob  -T /tmp/vR10W27JBX/isec.tab.gz /tmp/vR10W27JBX/isec.a.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vR10W27JBX/isec-miss.1.1.vcf.gz /tmp/vR10W27JBX/isec-miss.1.2.vcf.gz /tmp/vR10W27JBX/isec-miss.1.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vR10W27JBX/isec-miss.1.1.vcf.gz /tmp/vR10W27JBX/isec-miss.1.2.vcf.gz /tmp/vR10W27JBX/isec-miss.1.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/isec-miss.1.regs.txt -n +1 /tmp/vR10W27JBX/isec-miss.1.1.vcf.gz /tmp/vR10W27JBX/isec-miss.1.2.vcf.gz /tmp/vR10W27JBX/isec-miss.1.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/isec-miss.1.regs.txt -n +1 /tmp/vR10W27JBX/isec-miss.1.1.vcf.gz /tmp/vR10W27JBX/isec-miss.1.2.vcf.gz /tmp/vR10W27JBX/isec-miss.1.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vR10W27JBX/isec-miss.2.1.vcf.gz /tmp/vR10W27JBX/isec-miss.2.2.vcf.gz /tmp/vR10W27JBX/isec-miss.2.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vR10W27JBX/isec-miss.2.1.vcf.gz /tmp/vR10W27JBX/isec-miss.2.2.vcf.gz /tmp/vR10W27JBX/isec-miss.2.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/isec-miss.1.regs.txt -n +1 /tmp/vR10W27JBX/isec-miss.2.1.vcf.gz /tmp/vR10W27JBX/isec-miss.2.2.vcf.gz /tmp/vR10W27JBX/isec-miss.2.3.vcf.gz
616s .. ok
616s 
616s test_vcf_isec:
616s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools isec -Ob -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/isec-miss.1.regs.txt -n +1 /tmp/vR10W27JBX/isec-miss.2.1.vcf.gz /tmp/vR10W27JBX/isec-miss.2.2.vcf.gz /tmp/vR10W27JBX/isec-miss.2.3.vcf.gz
616s .. ok
616s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -i AF:join /tmp/vR10W27JBX/merge.join.a.vcf.gz /tmp/vR10W27JBX/merge.join.b.vcf.gz
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -i AF:join /tmp/vR10W27JBX/merge.join.a.vcf.gz /tmp/vR10W27JBX/merge.join.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -i AF:join /tmp/vR10W27JBX/merge.join.a.bcf /tmp/vR10W27JBX/merge.join.b.bcf
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -i AF:join /tmp/vR10W27JBX/merge.join.a.bcf /tmp/vR10W27JBX/merge.join.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 1 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 1 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 2 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 2 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
617s .. ok
617s 
617s test_vcf_merge:
617s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 3 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 3 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 4 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 4 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 5 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/vR10W27JBX/merge.LPL.a.vcf.gz /tmp/vR10W27JBX/merge.LPL.b.vcf.gz /tmp/vR10W27JBX/merge.LPL.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -L 5 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/vR10W27JBX/merge.LPL.a.bcf /tmp/vR10W27JBX/merge.LPL.b.bcf /tmp/vR10W27JBX/merge.LPL.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples /tmp/vR10W27JBX/merge.a.vcf.gz /tmp/vR10W27JBX/merge.b.vcf.gz /tmp/vR10W27JBX/merge.c.vcf.gz
618s .. ok
618s 
618s test_vcf_merge:
618s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples /tmp/vR10W27JBX/merge.a.vcf.gz /tmp/vR10W27JBX/merge.b.vcf.gz /tmp/vR10W27JBX/merge.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
618s .. ok
618s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples /tmp/vR10W27JBX/merge.a.bcf /tmp/vR10W27JBX/merge.b.bcf /tmp/vR10W27JBX/merge.c.bcf
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples /tmp/vR10W27JBX/merge.a.bcf /tmp/vR10W27JBX/merge.b.bcf /tmp/vR10W27JBX/merge.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -Fx /tmp/vR10W27JBX/merge.a.vcf.gz /tmp/vR10W27JBX/merge.b.vcf.gz /tmp/vR10W27JBX/merge.c.vcf.gz
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -Fx /tmp/vR10W27JBX/merge.a.vcf.gz /tmp/vR10W27JBX/merge.b.vcf.gz /tmp/vR10W27JBX/merge.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -Fx /tmp/vR10W27JBX/merge.a.bcf /tmp/vR10W27JBX/merge.b.bcf /tmp/vR10W27JBX/merge.c.bcf
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -Fx /tmp/vR10W27JBX/merge.a.bcf /tmp/vR10W27JBX/merge.b.bcf /tmp/vR10W27JBX/merge.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -0 /tmp/vR10W27JBX/merge.a.vcf.gz /tmp/vR10W27JBX/merge.b.vcf.gz /tmp/vR10W27JBX/merge.c.vcf.gz
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -0 /tmp/vR10W27JBX/merge.a.vcf.gz /tmp/vR10W27JBX/merge.b.vcf.gz /tmp/vR10W27JBX/merge.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -0 /tmp/vR10W27JBX/merge.a.bcf /tmp/vR10W27JBX/merge.b.bcf /tmp/vR10W27JBX/merge.c.bcf
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -0 /tmp/vR10W27JBX/merge.a.bcf /tmp/vR10W27JBX/merge.b.bcf /tmp/vR10W27JBX/merge.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m none /tmp/vR10W27JBX/merge.2.a.vcf.gz /tmp/vR10W27JBX/merge.2.b.vcf.gz
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m none /tmp/vR10W27JBX/merge.2.a.vcf.gz /tmp/vR10W27JBX/merge.2.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m none /tmp/vR10W27JBX/merge.2.a.bcf /tmp/vR10W27JBX/merge.2.b.bcf
619s .. ok
619s 
619s test_vcf_merge:
619s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m none /tmp/vR10W27JBX/merge.2.a.bcf /tmp/vR10W27JBX/merge.2.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m both /tmp/vR10W27JBX/merge.2.a.vcf.gz /tmp/vR10W27JBX/merge.2.b.vcf.gz
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m both /tmp/vR10W27JBX/merge.2.a.vcf.gz /tmp/vR10W27JBX/merge.2.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m both /tmp/vR10W27JBX/merge.2.a.bcf /tmp/vR10W27JBX/merge.2.b.bcf
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m both /tmp/vR10W27JBX/merge.2.a.bcf /tmp/vR10W27JBX/merge.2.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m all /tmp/vR10W27JBX/merge.2.a.vcf.gz /tmp/vR10W27JBX/merge.2.b.vcf.gz
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m all /tmp/vR10W27JBX/merge.2.a.vcf.gz /tmp/vR10W27JBX/merge.2.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m all /tmp/vR10W27JBX/merge.2.a.bcf /tmp/vR10W27JBX/merge.2.b.bcf
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m all /tmp/vR10W27JBX/merge.2.a.bcf /tmp/vR10W27JBX/merge.2.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vR10W27JBX/merge.3.a.vcf.gz /tmp/vR10W27JBX/merge.3.b.vcf.gz
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vR10W27JBX/merge.3.a.vcf.gz /tmp/vR10W27JBX/merge.3.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vR10W27JBX/merge.3.a.bcf /tmp/vR10W27JBX/merge.3.b.bcf
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vR10W27JBX/merge.3.a.bcf /tmp/vR10W27JBX/merge.3.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m id /tmp/vR10W27JBX/merge.4.a.vcf.gz /tmp/vR10W27JBX/merge.4.b.vcf.gz
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m id /tmp/vR10W27JBX/merge.4.a.vcf.gz /tmp/vR10W27JBX/merge.4.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples -m id /tmp/vR10W27JBX/merge.4.a.bcf /tmp/vR10W27JBX/merge.4.b.bcf
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples -m id /tmp/vR10W27JBX/merge.4.a.bcf /tmp/vR10W27JBX/merge.4.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/gvcf.merge.1.vcf.gz /tmp/vR10W27JBX/gvcf.merge.2.vcf.gz /tmp/vR10W27JBX/gvcf.merge.3.vcf.gz
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/gvcf.merge.1.vcf.gz /tmp/vR10W27JBX/gvcf.merge.2.vcf.gz /tmp/vR10W27JBX/gvcf.merge.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
620s .. ok
620s 
620s test_vcf_merge:
620s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/gvcf.merge.1.bcf /tmp/vR10W27JBX/gvcf.merge.2.bcf /tmp/vR10W27JBX/gvcf.merge.3.bcf
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/gvcf.merge.1.bcf /tmp/vR10W27JBX/gvcf.merge.2.bcf /tmp/vR10W27JBX/gvcf.merge.3.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.c.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - -m both,* /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.c.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - -m both,** /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.c.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.2.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - -i SRC:join /tmp/vR10W27JBX/merge.gvcf.3.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.3.b.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/vR10W27JBX/merge.gvcf.3.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.3.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.4.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.4.b.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.4.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.4.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.4.a.bcf /tmp/vR10W27JBX/merge.gvcf.4.b.bcf
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.4.a.bcf /tmp/vR10W27JBX/merge.gvcf.4.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.5.a.vcf.gz /tmp/vR10W27JBX/merge.5.b.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.5.a.vcf.gz /tmp/vR10W27JBX/merge.5.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.5.a.bcf /tmp/vR10W27JBX/merge.5.b.bcf
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.5.a.bcf /tmp/vR10W27JBX/merge.5.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.6.a.vcf.gz /tmp/vR10W27JBX/merge.6.b.vcf.gz
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.6.a.vcf.gz /tmp/vR10W27JBX/merge.6.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.6.a.bcf /tmp/vR10W27JBX/merge.6.b.bcf
621s .. ok
621s 
621s test_vcf_merge:
621s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.6.a.bcf /tmp/vR10W27JBX/merge.6.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.7.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.7.b.vcf.gz
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.7.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.7.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.7.a.bcf /tmp/vR10W27JBX/merge.gvcf.7.b.bcf
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.7.a.bcf /tmp/vR10W27JBX/merge.gvcf.7.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.8.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.8.b.vcf.gz
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.8.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.8.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.8.a.bcf /tmp/vR10W27JBX/merge.gvcf.8.b.bcf
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.8.a.bcf /tmp/vR10W27JBX/merge.gvcf.8.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples /tmp/vR10W27JBX/merge.7.a.vcf.gz /tmp/vR10W27JBX/merge.7.b.vcf.gz
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples /tmp/vR10W27JBX/merge.7.a.vcf.gz /tmp/vR10W27JBX/merge.7.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --force-samples /tmp/vR10W27JBX/merge.7.a.bcf /tmp/vR10W27JBX/merge.7.b.bcf
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --force-samples /tmp/vR10W27JBX/merge.7.a.bcf /tmp/vR10W27JBX/merge.7.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz
622s .. ok
622s 
622s test_vcf_merge:
622s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
622s .. ok
622s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9e.vcf.gz
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9e.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf /tmp/vR10W27JBX/merge.gvcf.9e.bcf
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf /tmp/vR10W27JBX/merge.gvcf.9e.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9e.vcf.gz
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9c.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9d.vcf.gz /tmp/vR10W27JBX/merge.gvcf.9e.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf /tmp/vR10W27JBX/merge.gvcf.9e.bcf
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa -r 22:21-23 /tmp/vR10W27JBX/merge.gvcf.9a.bcf /tmp/vR10W27JBX/merge.gvcf.9b.bcf /tmp/vR10W27JBX/merge.gvcf.9c.bcf /tmp/vR10W27JBX/merge.gvcf.9d.bcf /tmp/vR10W27JBX/merge.gvcf.9e.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m none /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m none /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
623s .. ok
623s 
623s test_vcf_merge:
623s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m none /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m none /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa -m none /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa -m none /tmp/vR10W27JBX/merge.gvcf.10.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa -m none /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.gvcf.10.fa -m none /tmp/vR10W27JBX/merge.gvcf.10.a.bcf /tmp/vR10W27JBX/merge.gvcf.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.noidx.a.vcf.gz /tmp/vR10W27JBX/merge.noidx.b.vcf.gz /tmp/vR10W27JBX/merge.noidx.c.vcf.gz
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.noidx.a.vcf.gz /tmp/vR10W27JBX/merge.noidx.b.vcf.gz /tmp/vR10W27JBX/merge.noidx.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.noidx.a.bcf /tmp/vR10W27JBX/merge.noidx.b.bcf /tmp/vR10W27JBX/merge.noidx.c.bcf
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.noidx.a.bcf /tmp/vR10W27JBX/merge.noidx.b.bcf /tmp/vR10W27JBX/merge.noidx.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --no-index /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.noidx.a.vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.noidx.b.vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.noidx.c.vcf
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --no-index /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.noidx.a.vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.noidx.b.vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/merge.noidx.c.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --no-index /tmp/vR10W27JBX/merge.noidx.a.bcf /tmp/vR10W27JBX/merge.noidx.b.bcf /tmp/vR10W27JBX/merge.noidx.c.bcf
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --no-index /tmp/vR10W27JBX/merge.noidx.a.bcf /tmp/vR10W27JBX/merge.noidx.b.bcf /tmp/vR10W27JBX/merge.noidx.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.8.a.vcf.gz /tmp/vR10W27JBX/merge.8.b.vcf.gz
624s .. ok
624s 
624s test_vcf_merge:
624s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.8.a.vcf.gz /tmp/vR10W27JBX/merge.8.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
624s .. ok
624s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.8.a.bcf /tmp/vR10W27JBX/merge.8.b.bcf
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.8.a.bcf /tmp/vR10W27JBX/merge.8.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.8.a.vcf.gz /tmp/vR10W27JBX/merge.8.b.vcf.gz
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.8.a.vcf.gz /tmp/vR10W27JBX/merge.8.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.8.a.bcf /tmp/vR10W27JBX/merge.8.b.bcf
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.8.a.bcf /tmp/vR10W27JBX/merge.8.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.9.a.vcf.gz /tmp/vR10W27JBX/merge.9.b.vcf.gz
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.9.a.vcf.gz /tmp/vR10W27JBX/merge.9.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version  /tmp/vR10W27JBX/merge.9.a.bcf /tmp/vR10W27JBX/merge.9.b.bcf
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob  /tmp/vR10W27JBX/merge.9.a.bcf /tmp/vR10W27JBX/merge.9.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.9.a.vcf.gz /tmp/vR10W27JBX/merge.9.b.vcf.gz
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.9.a.vcf.gz /tmp/vR10W27JBX/merge.9.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.9.a.bcf /tmp/vR10W27JBX/merge.9.b.bcf
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/vR10W27JBX/merge.9.a.bcf /tmp/vR10W27JBX/merge.9.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m none /tmp/vR10W27JBX/merge.10.a.vcf.gz /tmp/vR10W27JBX/merge.10.b.vcf.gz
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m none /tmp/vR10W27JBX/merge.10.a.vcf.gz /tmp/vR10W27JBX/merge.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m none /tmp/vR10W27JBX/merge.10.a.bcf /tmp/vR10W27JBX/merge.10.b.bcf
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m none /tmp/vR10W27JBX/merge.10.a.bcf /tmp/vR10W27JBX/merge.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m both /tmp/vR10W27JBX/merge.10.a.vcf.gz /tmp/vR10W27JBX/merge.10.b.vcf.gz
625s .. ok
625s 
625s test_vcf_merge:
625s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m both /tmp/vR10W27JBX/merge.10.a.vcf.gz /tmp/vR10W27JBX/merge.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
625s .. ok
625s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m both /tmp/vR10W27JBX/merge.10.a.bcf /tmp/vR10W27JBX/merge.10.b.bcf
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m both /tmp/vR10W27JBX/merge.10.a.bcf /tmp/vR10W27JBX/merge.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m snp-ins-del /tmp/vR10W27JBX/merge.10.a.vcf.gz /tmp/vR10W27JBX/merge.10.b.vcf.gz
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m snp-ins-del /tmp/vR10W27JBX/merge.10.a.vcf.gz /tmp/vR10W27JBX/merge.10.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -m snp-ins-del /tmp/vR10W27JBX/merge.10.a.bcf /tmp/vR10W27JBX/merge.10.b.bcf
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob -m snp-ins-del /tmp/vR10W27JBX/merge.10.a.bcf /tmp/vR10W27JBX/merge.10.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.mrules.1.a.vcf.gz /tmp/vR10W27JBX/merge.mrules.1.b.vcf.gz
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.mrules.1.a.vcf.gz /tmp/vR10W27JBX/merge.mrules.1.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.mrules.1.a.bcf /tmp/vR10W27JBX/merge.mrules.1.b.bcf
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.mrules.1.a.bcf /tmp/vR10W27JBX/merge.mrules.1.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/vR10W27JBX/merge.mrules.1.a.vcf.gz /tmp/vR10W27JBX/merge.mrules.1.b.vcf.gz
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/vR10W27JBX/merge.mrules.1.a.vcf.gz /tmp/vR10W27JBX/merge.mrules.1.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/vR10W27JBX/merge.mrules.1.a.bcf /tmp/vR10W27JBX/merge.mrules.1.b.bcf
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/vR10W27JBX/merge.mrules.1.a.bcf /tmp/vR10W27JBX/merge.mrules.1.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.5.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.5.b.vcf.gz
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.5.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.5.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.5.a.bcf /tmp/vR10W27JBX/merge.gvcf.5.b.bcf
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.5.a.bcf /tmp/vR10W27JBX/merge.gvcf.5.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - --merge none /tmp/vR10W27JBX/merge.gvcf.5.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.5.b.vcf.gz
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/vR10W27JBX/merge.gvcf.5.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.5.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - --merge none /tmp/vR10W27JBX/merge.gvcf.5.a.bcf /tmp/vR10W27JBX/merge.gvcf.5.b.bcf
626s .. ok
626s 
626s test_vcf_merge:
626s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/vR10W27JBX/merge.gvcf.5.a.bcf /tmp/vR10W27JBX/merge.gvcf.5.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
626s .. ok
626s 
627s test_vcf_merge:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.11.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.11.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.11.c.vcf.gz
627s .. ok
627s 
627s test_vcf_merge:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.11.a.vcf.gz /tmp/vR10W27JBX/merge.gvcf.11.b.vcf.gz /tmp/vR10W27JBX/merge.gvcf.11.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
627s .. ok
627s 
627s test_vcf_merge:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version --gvcf - /tmp/vR10W27JBX/merge.gvcf.11.a.bcf /tmp/vR10W27JBX/merge.gvcf.11.b.bcf /tmp/vR10W27JBX/merge.gvcf.11.c.bcf
627s .. ok
627s 
627s test_vcf_merge:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools merge --no-version -Ob --gvcf - /tmp/vR10W27JBX/merge.gvcf.11.a.bcf /tmp/vR10W27JBX/merge.gvcf.11.b.bcf /tmp/vR10W27JBX/merge.gvcf.11.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version | grep -v ^##bcftools_
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/vR10W27JBX/query.string.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.string.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/vR10W27JBX/query.string.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.string.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/vR10W27JBX/query.string.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.string.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.string.2.1.txt' /tmp/vR10W27JBX/query.string.2.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.string.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.string.2.1.txt'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.string.2.2.txt' /tmp/vR10W27JBX/query.string.2.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.string.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.string.2.2.txt'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/vR10W27JBX/query.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%RSX\t%VKX\n' /tmp/vR10W27JBX/query.variantkey.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.variantkey.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%RSX\t%VKX\n'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/vR10W27JBX/view.filter.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/vR10W27JBX/query.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/vR10W27JBX/query.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/vR10W27JBX/query.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/vR10W27JBX/query.vcf.gz
627s .. ok
627s 
627s test_vcf_query:
627s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/vR10W27JBX/view.filter.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/vR10W27JBX/query.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/vR10W27JBX/query.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/vR10W27JBX/query.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/vR10W27JBX/query.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/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/vR10W27JBX/view.vectors.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.vectors.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/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'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/vR10W27JBX/query.filter.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/vR10W27JBX/query.filter.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/vR10W27JBX/query.filter.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/vR10W27JBX/query.filter.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/vR10W27JBX/query.2.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IINT="."'  -f'%POS %IINT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IINT="."'  -f'%POS %IINT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IINT="."'  -f'%POS %IINT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IINT="."'  -f'%POS %IINT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n'
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/vR10W27JBX/missing.vcf.gz
628s .. ok
628s 
628s test_vcf_query:
628s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/vR10W27JBX/missing.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/vR10W27JBX/filter.11.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/vR10W27JBX/filter.11.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/vR10W27JBX/filter.11.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/vR10W27JBX/filter.11.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%LINE' /tmp/vR10W27JBX/query.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%LINE'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/vR10W27JBX/query.filter-type.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter-type.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/vR10W27JBX/query.filter-type.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter-type.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/vR10W27JBX/query.filter-type.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter-type.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/vR10W27JBX/query.filter-type.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter-type.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/vR10W27JBX/query.filter-type.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter-type.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/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/vR10W27JBX/filter-missing-floats.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter-missing-floats.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/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'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/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/vR10W27JBX/filter-missing-floats.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter-missing-floats.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/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'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/vR10W27JBX/missing.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/vR10W27JBX/query.filter.2.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."'
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/vR10W27JBX/view.filter.vcf.gz
629s .. ok
629s 
629s test_vcf_query:
629s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/vR10W27JBX/filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/vR10W27JBX/filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/vR10W27JBX/view.filter.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.filter.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/vR10W27JBX/query.filter.3.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"' /tmp/vR10W27JBX/query.filter.3.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/vR10W27JBX/query.filter.3.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/vR10W27JBX/filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/vR10W27JBX/query.filter.4.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%ID\n' -i 'ID=@/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.56.out' /tmp/vR10W27JBX/view.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/view.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%ID\n' -i 'ID=@/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.56.out'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/vR10W27JBX/query.filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/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/vR10W27JBX/query.filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/vR10W27JBX/query.filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/vR10W27JBX/query.filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/vR10W27JBX/query.filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/vR10W27JBX/query.filter.5.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/vR10W27JBX/query.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/vR10W27JBX/query.negative.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.negative.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/vR10W27JBX/query.negative.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.negative.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)'
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/vR10W27JBX/query.negative.vcf.gz
630s .. ok
630s 
630s test_vcf_query:
630s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.negative.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/vR10W27JBX/query.negative.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.negative.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/vR10W27JBX/query.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/vR10W27JBX/query.filter.11.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/vR10W27JBX/query.filter.11.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/vR10W27JBX/query.filter.11.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/vR10W27JBX/query.filter.11.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/vR10W27JBX/query.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/vR10W27JBX/query.filter.6.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.6.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/vR10W27JBX/query.filter.7.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.7.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/vR10W27JBX/query.filter.8.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.8.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/vR10W27JBX/query.filter.8.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.8.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/vR10W27JBX/query.filter.9.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.9.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/vR10W27JBX/query.filter.9.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.9.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]'
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/vR10W27JBX/query.filter.13.vcf.gz
631s .. ok
631s 
631s test_vcf_query:
631s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.13.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5'
631s .. ok
631s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/vR10W27JBX/query.filter.10.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.10.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/vR10W27JBX/query.filter.10.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.10.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/vR10W27JBX/query.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/vR10W27JBX/query.filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/vR10W27JBX/query.filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt /tmp/vR10W27JBX/query.smpl.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.smpl.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -l -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt /tmp/vR10W27JBX/query.smpl.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.smpl.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -l -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f "[%SAMPLE %GT\n]" -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt /tmp/vR10W27JBX/query.smpl.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.smpl.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f "[%SAMPLE %GT\n]" -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -l -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt /tmp/vR10W27JBX/query.smpl.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.smpl.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -l -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.11.txt
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.txt /tmp/vR10W27JBX/query.smpl.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.smpl.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f "[%SAMPLE %GT\n]" -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.txt
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -l -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.txt /tmp/vR10W27JBX/query.smpl.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.smpl.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -l -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/query.smpl.txt
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/vR10W27JBX/query.filter.id.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.id.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%ID\n' -i'ID~"s12"'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/vR10W27JBX/query.filter.id.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.filter.id.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%ID\n' -i'ID="rs123"'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/vR10W27JBX/filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="A"' -f'%FILTER\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/vR10W27JBX/filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER~"A"' -f'%FILTER\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/vR10W27JBX/filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER="A;B"' -f'%FILTER\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/vR10W27JBX/filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/vR10W27JBX/filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/vR10W27JBX/filter.12.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.12.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n'
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/vR10W27JBX/filter.10.vcf.gz
632s .. ok
632s 
632s test_vcf_query:
632s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.10.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'DP%10==2' -f'[ %DP]\n'
632s .. ok
632s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/vR10W27JBX/filter.13.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/filter.13.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n'
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]' /tmp/vR10W27JBX/query.header.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.header.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\n]'
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n' /tmp/vR10W27JBX/query.header.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.header.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'[%CHROM %POS  %SAMPLE %DP %GT\t]\n'
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/vR10W27JBX/query.header.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.header.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n'
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/vR10W27JBX/query.header.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.header.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]'
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/vR10W27JBX/query.header.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.header.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n'
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/vR10W27JBX/query.header.vcf.gz
633s .. ok
633s 
633s test_vcf_query:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/query.header.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]'
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -cx -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -cx -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m- /tmp/vR10W27JBX/norm.split.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m- /tmp/vR10W27JBX/norm.split.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m- /tmp/vR10W27JBX/norm.split.2.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m- /tmp/vR10W27JBX/norm.split.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m- --force /tmp/vR10W27JBX/norm.split.3.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m- --force /tmp/vR10W27JBX/norm.split.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m- /tmp/vR10W27JBX/norm.split.4.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m- /tmp/vR10W27JBX/norm.split.4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m- --keep-sum AD /tmp/vR10W27JBX/norm.split.4.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m- --keep-sum AD /tmp/vR10W27JBX/norm.split.4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m- -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.split.vcf.gz
633s .. ok
633s 
633s test_vcf_norm:
633s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m- -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.split.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
633s .. ok
633s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m+ /tmp/vR10W27JBX/norm.merge.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m+ /tmp/vR10W27JBX/norm.merge.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m+ /tmp/vR10W27JBX/norm.merge.2.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m+ /tmp/vR10W27JBX/norm.merge.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m+ /tmp/vR10W27JBX/norm.merge.3.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m+ /tmp/vR10W27JBX/norm.merge.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m+ -s /tmp/vR10W27JBX/norm.merge.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m+ -s /tmp/vR10W27JBX/norm.merge.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -Nc s -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.setref.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -Nc s -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.setref.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.telomere.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.fa /tmp/vR10W27JBX/norm.telomere.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d snps /tmp/vR10W27JBX/norm.rmdup.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d snps /tmp/vR10W27JBX/norm.rmdup.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d indels /tmp/vR10W27JBX/norm.rmdup.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d indels /tmp/vR10W27JBX/norm.rmdup.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d both /tmp/vR10W27JBX/norm.rmdup.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d both /tmp/vR10W27JBX/norm.rmdup.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d all /tmp/vR10W27JBX/norm.rmdup.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d all /tmp/vR10W27JBX/norm.rmdup.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d none /tmp/vR10W27JBX/norm.rmdup.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d none /tmp/vR10W27JBX/norm.rmdup.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d exact /tmp/vR10W27JBX/norm.rmdup.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d exact /tmp/vR10W27JBX/norm.rmdup.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d none /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d none /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d exact /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d exact /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
634s .. ok
634s 
634s test_vcf_norm:
634s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d indels /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d indels /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d any /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d any /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d both /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d both /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -d snps /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -d snps /tmp/vR10W27JBX/norm.rmdup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -c s -a -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.2.fa /tmp/vR10W27JBX/norm.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -c s -a -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.2.fa /tmp/vR10W27JBX/norm.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -c s -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.iupac.fa /tmp/vR10W27JBX/norm.iupac.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -c s -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.iupac.fa /tmp/vR10W27JBX/norm.iupac.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -c s -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.3.fa /tmp/vR10W27JBX/norm.3.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -c s -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.3.fa /tmp/vR10W27JBX/norm.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC -m -any /tmp/vR10W27JBX/atomize.split.1.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC -m -any /tmp/vR10W27JBX/atomize.split.1.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.1.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.1.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.1.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.1.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.2.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --atom-overlaps . /tmp/vR10W27JBX/atomize.split.3.vcf.gz
635s .. ok
635s 
635s test_vcf_norm:
635s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --atom-overlaps . /tmp/vR10W27JBX/atomize.split.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
635s .. ok
635s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.4.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vR10W27JBX/atomize.split.4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m +both /tmp/vR10W27JBX/norm.4.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m +both /tmp/vR10W27JBX/norm.4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m +any /tmp/vR10W27JBX/norm.4.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m +any /tmp/vR10W27JBX/norm.4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m - --multi-overlaps 0 /tmp/vR10W27JBX/norm.5.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m - --multi-overlaps 0 /tmp/vR10W27JBX/norm.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m - --multi-overlaps . /tmp/vR10W27JBX/norm.5.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m - --multi-overlaps . /tmp/vR10W27JBX/norm.5.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m -any /tmp/vR10W27JBX/norm.m-any.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m -any /tmp/vR10W27JBX/norm.m-any.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m -any /tmp/vR10W27JBX/norm.phased-split.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m -any /tmp/vR10W27JBX/norm.phased-split.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  -m +any /tmp/vR10W27JBX/norm.phased-join.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  -m +any /tmp/vR10W27JBX/norm.phased-join.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --old-rec-tag ORI -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.symbolic.fa /tmp/vR10W27JBX/norm.symbolic.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --old-rec-tag ORI -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.symbolic.fa /tmp/vR10W27JBX/norm.symbolic.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --old-rec-tag ORI -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.symbolic.fa /tmp/vR10W27JBX/norm.symbolic.2.vcf.gz
636s .. ok
636s 
636s test_vcf_norm:
636s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --old-rec-tag ORI -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.symbolic.fa /tmp/vR10W27JBX/norm.symbolic.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
636s .. ok
636s 
637s test_vcf_norm:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --old-rec-tag ORI -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.right-align.fa /tmp/vR10W27JBX/norm.right-align.vcf.gz
637s .. ok
637s 
637s test_vcf_norm:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --old-rec-tag ORI -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.right-align.fa /tmp/vR10W27JBX/norm.right-align.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_norm:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm --no-version  --old-rec-tag ORI -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.right-align.gff -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.right-align.fa /tmp/vR10W27JBX/norm.right-align.vcf.gz
637s .. ok
637s 
637s test_vcf_norm:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools norm -Ob  --old-rec-tag ORI -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.right-align.gff -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/norm.right-align.fa /tmp/vR10W27JBX/norm.right-align.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -HA /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz 
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -HAA /tmp/vR10W27JBX/merge.gvcf.2.a.vcf.gz 
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1:1-2
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1:1-2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1:1,1:2
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1:1,1:2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1:1-1
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r 1:1-1 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1} | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}:1-2
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}:1-2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}:1-1
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1}:1-1 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1} | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}:1-2
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}:1-1
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}-2
637s .. ok, expected non-zero status
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/weird-chr-names.vcf.gz -r {1:1-1}-2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok, expected non-zero status
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/vR10W27JBX/view.vcf.gz 
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -f PASS -Xks NA00003 /tmp/vR10W27JBX/view.vcf.gz -r20,Y
637s .. ok
637s 
637s test_vcf_view:
637s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -f PASS -Xks NA00003 /tmp/vR10W27JBX/view.vcf.gz -r20,Y | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -xs NA00003 /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -xs NA00003 /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -p /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -p /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -P /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -P /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -Hu /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -GVsnps /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -GVsnps /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -s ^NA00003 /tmp/vR10W27JBX/view.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -s ^NA00003 /tmp/vR10W27JBX/view.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version  /tmp/vR10W27JBX/view.omitgenotypes.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob  /tmp/vR10W27JBX/view.omitgenotypes.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -G /tmp/vR10W27JBX/view.omitgenotypes.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -G /tmp/vR10W27JBX/view.omitgenotypes.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -HG /tmp/vR10W27JBX/view.omitgenotypes.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -a /tmp/vR10W27JBX/many.alleles.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -a /tmp/vR10W27JBX/many.alleles.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -asA /tmp/vR10W27JBX/view.vectors.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -asA /tmp/vR10W27JBX/view.vectors.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -asB /tmp/vR10W27JBX/view.vectors.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -asB /tmp/vR10W27JBX/view.vectors.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -asA /tmp/vR10W27JBX/view.vectors.2.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -asA /tmp/vR10W27JBX/view.vectors.2.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/vR10W27JBX/view.filter.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/vR10W27JBX/view.filter.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/vR10W27JBX/view.filter.vcf.gz 
638s .. ok
638s 
638s test_vcf_view:
638s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/vR10W27JBX/view.filter.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i'TXT0="text"' /tmp/vR10W27JBX/view.filter.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.chrs.tab /tmp/vR10W27JBX/view.chrs.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.chrs.tab /tmp/vR10W27JBX/view.chrs.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -i 'POS>=3062917' /tmp/vR10W27JBX/filter.2.vcf.gz 1:3062917-3157410
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -i 'POS>=3062917' /tmp/vR10W27JBX/filter.2.vcf.gz 1:3062917-3157410 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/vR10W27JBX/idx.1.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/vR10W27JBX/idx.2.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/idx.2.bed /tmp/vR10W27JBX/idx.2.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/idx.3.bed /tmp/vR10W27JBX/idx.3.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/idx.4.bed /tmp/vR10W27JBX/idx.4.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -Ht 2 /tmp/vR10W27JBX/view-t.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -Ht 3 /tmp/vR10W27JBX/view-t.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_view:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/vR10W27JBX/overlap.vcf.gz 
639s .. ok
639s 
639s test_vcf_64bit:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.1.vcf -H
639s .. ok
639s 
639s test_vcf_64bit:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.1.vcf     | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
639s .. ok
639s 
639s test_vcf_64bit:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.1.vcf -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
639s .. ok
639s 
639s test_vcf_64bit:
639s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.2.vcf -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.2.vcf     | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.2.vcf -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.3.vcf -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.3.vcf     | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.4.vcf -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.4.vcf     | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.4.vcf -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.5.vcf -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.5.vcf     | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_64bit:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view /tmp/autopkgtest.M9R37K/build.dgl/src/test/view64bit.5.vcf -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -C5:nonmajor /tmp/vR10W27JBX/view.minmaxac.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -c6:nonmajor /tmp/vR10W27JBX/view.minmaxac.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -q0.3:major /tmp/vR10W27JBX/view.minmaxac.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/vR10W27JBX/view.filter.annovar.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/vR10W27JBX/view.filter.annovar.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/vR10W27JBX/view.filter.annovar.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -H -a /tmp/vR10W27JBX/view-a.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.sites.txt /tmp/vR10W27JBX/view.sites.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.sites.txt /tmp/vR10W27JBX/view.sites.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.sites.txt.gz /tmp/vR10W27JBX/view.sites.vcf.gz 
640s .. ok
640s 
640s test_vcf_view:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.sites.txt.gz /tmp/vR10W27JBX/view.sites.vcf.gz  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
640s .. ok
640s 
640s test_vcf_head:
640s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -h 0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -h 1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -h 5 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -h 22 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -h 23 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -n 0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -n 1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -n 5 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -h 5 -n 5 < /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
641s .. ok
641s 
641s test_vcf_head2:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -s0 /tmp/vR10W27JBX/mpileup.2.vcf.gz
641s .. ok
641s 
641s test_vcf_head2:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -Ob /tmp/vR10W27JBX/mpileup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -s0
641s .. ok
641s 
641s test_vcf_head2:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -s1 /tmp/vR10W27JBX/mpileup.2.vcf.gz
641s .. ok
641s 
641s test_vcf_head2:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -Ob /tmp/vR10W27JBX/mpileup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -s1
641s .. ok
641s 
641s test_vcf_head2:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -s2 -h2 /tmp/vR10W27JBX/mpileup.2.vcf.gz
641s .. ok
641s 
641s test_vcf_head2:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version -Ob /tmp/vR10W27JBX/mpileup.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools head -s2 -h2
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mg0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mg0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.4.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.4.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.5.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.5.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.X.vcf
641s .. ok
641s 
641s test_vcf_call:
641s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.X.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ped /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.X.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ped /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.X.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.X.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.X.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.NA19213.NA19129.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.NA19213.NA19129.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.NA19213.NA19129.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.NA19213.NA19129.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.samples --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.vcf
642s .. ok
642s 
642s test_vcf_call:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.samples --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.hwe.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.2.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.2.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.3.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.3.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.4.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.4.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.5.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.5.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.6.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.4.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.6.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.7.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.5.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.7.tab.gz -i /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.cals.1.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.cals.1.vcf
642s .. ok
642s 
642s test_vcf_call_cAls:
642s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.cals.1.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.cals.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
642s .. ok
642s 
643s test_vcf_call_cAls:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mA -C alleles -T /tmp/vR10W27JBX/mpileup.cals.2.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.cals.2.vcf
643s .. ok
643s 
643s test_vcf_call_cAls:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mA -C alleles -T /tmp/vR10W27JBX/mpileup.cals.2.tab.gz  /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.cals.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -cv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -cv /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.X.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ped /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.X.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ped /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -cv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.X.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -cv --ploidy-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.ploidy -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.2.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup.c.X.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/call-G.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv /tmp/autopkgtest.M9R37K/build.dgl/src/test/call-G.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -G - --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/call-G.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -G - --group-samples-tag AD /tmp/autopkgtest.M9R37K/build.dgl/src/test/call-G.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -mv -F AN_POP,AC_POP /tmp/autopkgtest.M9R37K/build.dgl/src/test/call-G.2.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -mv -F AN_POP,AC_POP /tmp/autopkgtest.M9R37K/build.dgl/src/test/call-G.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -m -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.txt /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -m -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.txt /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call --no-version -m -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.txt -a GP,GQ /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.vcf
643s .. ok
643s 
643s test_vcf_call:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools call -Ob -m -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.txt -a GP,GQ /tmp/autopkgtest.M9R37K/build.dgl/src/test/call.af-fixation.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'TXT0="text"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'TXT0="text"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | grep -v ^##bcftools_
643s .. ok
643s 
643s test_vcf_filter:
643s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'FMT/STR="XX"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'FMT/STR="XX"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S. -e'FMT/FILTER="aaa"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.2.vcf | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/view.filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -mx -g2 -G2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -mx -g2 -G2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'INFO/DP=19' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'INFO/DP=19' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'INFO/DP=19' -s XX /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'INFO/DP=19' -s XX /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'INFO/DP=19' -s XX -m+ /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'INFO/DP=19' -s XX -mx /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'INFO/DP=19' -s XX -m+x /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'FMT/GT="0/2"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'FMT/GT="0/2"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'FMT/GT="0/2"' -s XX /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'ALT="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'ALT="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%AC[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -i 'FORMAT/TEST3<25' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.4.vcf | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -i 'FORMAT/TEST4<25' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.4.vcf | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="A"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="A"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="RR"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="RR"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="RA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="RA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="AR"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="AR"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="AA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="AA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="aA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="aA"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="Aa"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="Aa"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="HOM"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="HOM"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="HET"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
644s .. ok
644s 
644s test_vcf_filter:
644s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="HET"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'GT="HAP"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'GT="HAP"' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%GT]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'AD[:1]=11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'AD[:1]=11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'AD[1:]=11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'AD[1:]=11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'FR[0:1]=11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%FR]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'FR[0:1]=11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%FR]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'AD[*]="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'AD[*]="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'AD[0:0]=="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'AD[0:0]=="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'AD[0:0]!="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'AD[0:0]!="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS[\t%AD]\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'QUAL=="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%QUAL\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'QUAL=="."' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\t%QUAL\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'N_PASS(DP>32)=1' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'N_PASS(DP>32)=1' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'F_PASS(DP>32)=0.5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'F_MISSING>=1/5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'F_MISSING>=1/5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'F_MISSING>=0.2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'F_MISSING>=0.2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%POS\n'
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -mx -s + -g2:mnp,indel,other /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.7.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.7.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'FORMAT/AO==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
645s .. ok
645s 
645s test_vcf_filter:
645s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i 'QUAL/FMT/AD==55' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.9.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.9.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i 'QUAL/INFO/AD==10' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.9.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.9.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -S . -e 'ABS(AO[1:])==2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.10.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_filter:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /tmp/autopkgtest.M9R37K/build.dgl/src/test/filter.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
646s .. ok
646s 
646s test_vcf_sort:
646s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools sort -m 0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/sort.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
647s .. ok
647s 
647s test_vcf_sort:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools sort -Ob -m 0 /tmp/autopkgtest.M9R37K/build.dgl/src/test/sort.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
647s .. ok
647s 
647s test_vcf_sort:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools sort -m 1000 /tmp/autopkgtest.M9R37K/build.dgl/src/test/sort.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
647s .. ok
647s 
647s test_vcf_sort:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools sort -Ob -m 1000 /tmp/autopkgtest.M9R37K/build.dgl/src/test/sort.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/regions.tab /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/regions.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/autopkgtest.M9R37K/build.dgl/src/test/regions.tab
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/autopkgtest.M9R37K/build.dgl/src/test/regions.tab /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vR10W27JBX/regions.tab.gz /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/regions.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vR10W27JBX/regions.tab.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vR10W27JBX/regions.tab.gz /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vR10W27JBX/regions.bed /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/regions.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vR10W27JBX/regions.bed
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vR10W27JBX/regions.bed /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vR10W27JBX/regions.bed.gz /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/regions.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vR10W27JBX/regions.bed.gz
647s .. ok
647s 
647s test_vcf_regions:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vR10W27JBX/regions.bed.gz /tmp/vR10W27JBX/regions.vcf.gz
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate2.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.hdr -c CHROM,POS,-,T_STR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate2.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.hdr -c CHROM,POS,-,T_STR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate2.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.hdr -c CHROM,FROM,TO,T_STR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate2.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.hdr -c CHROM,FROM,TO,T_STR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/vR10W27JBX/annotate.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/vR10W27JBX/annotate.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
647s .. ok
647s 
647s test_vcf_annotate:
647s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   -x FORMAT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   -x FORMAT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots4.vcf.gz  -c +INFO /tmp/vR10W27JBX/annotate4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots4.vcf.gz  -c +INFO /tmp/vR10W27JBX/annotate4.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots4.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots4.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots10.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate10.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots10.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate10.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots11.vcf.gz  -c FMT /tmp/vR10W27JBX/annotate11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots11.vcf.gz  -c FMT /tmp/vR10W27JBX/annotate11.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/vR10W27JBX/annotate2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots13.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.hdr -c CHROM,BEG,END,ABC /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots13.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.hdr -c CHROM,BEG,END,ABC /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots13.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots13.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots13.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots13.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate13.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   -x FILTER/XX,INFO/XX --force /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate14.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   -x FILTER/XX,INFO/XX --force /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate14.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate15.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate15.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
648s .. ok
648s 
648s test_vcf_annotate:
648s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate15.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate15.tab.gz -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate15.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate15.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate15.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   -x FILTER /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate16.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   -x FILTER /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate16.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate17.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate17.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate17.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate17.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate17.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate17.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate18.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate18.1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate18.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate18.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   -c INFO/FILTER:=FILTER /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate19.dst.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   -c INFO/FILTER:=FILTER /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate19.dst.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c INFO/FILTER:=./FILTER,FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=./FILTER /tmp/vR10W27JBX/annotate19.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate20.src.vcf.gz  -c  FMT/GT /tmp/vR10W27JBX/annotate20.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate20.src.vcf.gz  -c  FMT/GT /tmp/vR10W27JBX/annotate20.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate20.src.vcf.gz  -c +FMT/GT /tmp/vR10W27JBX/annotate20.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate20.src.vcf.gz  -c +FMT/GT /tmp/vR10W27JBX/annotate20.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
649s .. ok
649s 
649s test_vcf_annotate:
649s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate20.src.vcf.gz  -c -FMT/GT /tmp/vR10W27JBX/annotate20.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate20.src.vcf.gz  -c -FMT/GT /tmp/vR10W27JBX/annotate20.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.multi.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.multi.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate.missing-append.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate.missing-append.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate9.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate9.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   --rename-annots /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate21.txt /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate21.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   --rename-annots /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate21.txt /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate21.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/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.M9R37K/build.dgl/src/test/annotate21.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/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.M9R37K/build.dgl/src/test/annotate21.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/vR10W27JBX/annotate22.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/vR10W27JBX/annotate22.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate23.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate23.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate24.src.vcf.gz  -c XX /tmp/vR10W27JBX/annotate24.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate24.src.vcf.gz  -c XX /tmp/vR10W27JBX/annotate24.dst.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate25.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate25.tab.gz  -c CHROM,POS,ID,REF,ALT,~INFO/END /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate25.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate26.tab.gz  -c CHROM,POS,~POS /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate26.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate26.tab.gz  -c CHROM,POS,~POS /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate26.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate.missing.tab.gz  -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.missing.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
650s .. ok
650s 
650s test_vcf_annotate:
650s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.olap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.olap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.olap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.olap.tab.gz  -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.olap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.id.vcf.gz  -c ALT /tmp/vR10W27JBX/annotate.id.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.id.vcf.gz  -c ALT /tmp/vR10W27JBX/annotate.id.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.id.vcf.gz  -c +ALT /tmp/vR10W27JBX/annotate.id.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.id.vcf.gz  -c +ALT /tmp/vR10W27JBX/annotate.id.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/vR10W27JBX/annotate.id.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.id.2.vcf.gz  --pair-logic some -c +ID /tmp/vR10W27JBX/annotate.id.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/vR10W27JBX/annotate.id.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots.id.2.vcf.gz  --pair-logic any -c +ID /tmp/vR10W27JBX/annotate.id.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate27.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annotate27.tab.gz  -c CHROM,POS,REF,ALT,EVIDENCE /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate27.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots28.tab.gz  -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate28.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate   -m XXX /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob   -m XXX /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate34.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/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.M9R37K/build.dgl/src/test/annotate34.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -a /tmp/vR10W27JBX/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /tmp/autopkgtest.M9R37K/build.dgl/src/test/annots-mark.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
651s .. ok
651s 
651s test_vcf_annotate:
651s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate -Ob -a /tmp/vR10W27JBX/annots-mark.bed.gz  -c CHROM,FROM,TO -m TAG /tmp/autopkgtest.M9R37K/build.dgl/src/test/annots-mark.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version   /tmp/vR10W27JBX/concat.1.a.vcf.gz /tmp/vR10W27JBX/concat.1.b.vcf.gz
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob   /tmp/vR10W27JBX/concat.1.a.vcf.gz /tmp/vR10W27JBX/concat.1.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version   /tmp/vR10W27JBX/concat.1.a.bcf /tmp/vR10W27JBX/concat.1.b.bcf
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob   /tmp/vR10W27JBX/concat.1.a.bcf /tmp/vR10W27JBX/concat.1.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -a  /tmp/vR10W27JBX/concat.2.a.vcf.gz /tmp/vR10W27JBX/concat.2.b.vcf.gz
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -a  /tmp/vR10W27JBX/concat.2.a.vcf.gz /tmp/vR10W27JBX/concat.2.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -a  /tmp/vR10W27JBX/concat.2.a.bcf /tmp/vR10W27JBX/concat.2.b.bcf
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -a  /tmp/vR10W27JBX/concat.2.a.bcf /tmp/vR10W27JBX/concat.2.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -aD  /tmp/vR10W27JBX/concat.2.a.vcf.gz /tmp/vR10W27JBX/concat.2.b.vcf.gz
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -aD  /tmp/vR10W27JBX/concat.2.a.vcf.gz /tmp/vR10W27JBX/concat.2.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -aD  /tmp/vR10W27JBX/concat.2.a.bcf /tmp/vR10W27JBX/concat.2.b.bcf
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -aD  /tmp/vR10W27JBX/concat.2.a.bcf /tmp/vR10W27JBX/concat.2.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l --ligate-warn  /tmp/vR10W27JBX/concat.3.a.vcf.gz /tmp/vR10W27JBX/concat.3.b.vcf.gz /tmp/vR10W27JBX/concat.3.0.vcf.gz /tmp/vR10W27JBX/concat.3.c.vcf.gz /tmp/vR10W27JBX/concat.3.d.vcf.gz /tmp/vR10W27JBX/concat.3.e.vcf.gz /tmp/vR10W27JBX/concat.3.f.vcf.gz
652s .. ok
652s 
652s test_vcf_concat:
652s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l --ligate-warn  /tmp/vR10W27JBX/concat.3.a.vcf.gz /tmp/vR10W27JBX/concat.3.b.vcf.gz /tmp/vR10W27JBX/concat.3.0.vcf.gz /tmp/vR10W27JBX/concat.3.c.vcf.gz /tmp/vR10W27JBX/concat.3.d.vcf.gz /tmp/vR10W27JBX/concat.3.e.vcf.gz /tmp/vR10W27JBX/concat.3.f.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
653s .. ok
653s 
653s test_vcf_concat:
653s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l --ligate-warn  /tmp/vR10W27JBX/concat.3.a.bcf /tmp/vR10W27JBX/concat.3.b.bcf /tmp/vR10W27JBX/concat.3.0.bcf /tmp/vR10W27JBX/concat.3.c.bcf /tmp/vR10W27JBX/concat.3.d.bcf /tmp/vR10W27JBX/concat.3.e.bcf /tmp/vR10W27JBX/concat.3.f.bcf
653s .. ok
653s 
653s test_vcf_concat:
653s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l --ligate-warn  /tmp/vR10W27JBX/concat.3.a.bcf /tmp/vR10W27JBX/concat.3.b.bcf /tmp/vR10W27JBX/concat.3.0.bcf /tmp/vR10W27JBX/concat.3.c.bcf /tmp/vR10W27JBX/concat.3.d.bcf /tmp/vR10W27JBX/concat.3.e.bcf /tmp/vR10W27JBX/concat.3.f.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
653s Random seed for test_naive_concat: 2989599686
653s .. ok
653s 
656s test_naive_concat:
656s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --naive-force /tmp/vR10W27JBX/naive_concat.0.bcf /tmp/vR10W27JBX/naive_concat.1.bcf /tmp/vR10W27JBX/naive_concat.2.bcf /tmp/vR10W27JBX/naive_concat.3.bcf /tmp/vR10W27JBX/naive_concat.4.bcf /tmp/vR10W27JBX/naive_concat.5.bcf /tmp/vR10W27JBX/naive_concat.6.bcf /tmp/vR10W27JBX/naive_concat.7.bcf /tmp/vR10W27JBX/naive_concat.8.bcf /tmp/vR10W27JBX/naive_concat.9.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
656s .. ok
656s 
656s test_naive_concat:
656s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --naive /tmp/vR10W27JBX/naive_concat.0.vcf.gz /tmp/vR10W27JBX/naive_concat.1.vcf.gz /tmp/vR10W27JBX/naive_concat.2.vcf.gz /tmp/vR10W27JBX/naive_concat.3.vcf.gz /tmp/vR10W27JBX/naive_concat.4.vcf.gz /tmp/vR10W27JBX/naive_concat.5.vcf.gz /tmp/vR10W27JBX/naive_concat.6.vcf.gz /tmp/vR10W27JBX/naive_concat.7.vcf.gz /tmp/vR10W27JBX/naive_concat.8.vcf.gz /tmp/vR10W27JBX/naive_concat.9.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -H
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l  /tmp/vR10W27JBX/concat.4.a.vcf.gz /tmp/vR10W27JBX/concat.4.b.vcf.gz
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l  /tmp/vR10W27JBX/concat.4.a.vcf.gz /tmp/vR10W27JBX/concat.4.b.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l  /tmp/vR10W27JBX/concat.4.a.bcf /tmp/vR10W27JBX/concat.4.b.bcf
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l  /tmp/vR10W27JBX/concat.4.a.bcf /tmp/vR10W27JBX/concat.4.b.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l --ligate-warn  /tmp/vR10W27JBX/concat.5.a.vcf.gz /tmp/vR10W27JBX/concat.5.b.vcf.gz /tmp/vR10W27JBX/concat.5.c.vcf.gz
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l --ligate-warn  /tmp/vR10W27JBX/concat.5.a.vcf.gz /tmp/vR10W27JBX/concat.5.b.vcf.gz /tmp/vR10W27JBX/concat.5.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l --ligate-warn  /tmp/vR10W27JBX/concat.5.a.bcf /tmp/vR10W27JBX/concat.5.b.bcf /tmp/vR10W27JBX/concat.5.c.bcf
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l --ligate-warn  /tmp/vR10W27JBX/concat.5.a.bcf /tmp/vR10W27JBX/concat.5.b.bcf /tmp/vR10W27JBX/concat.5.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -l --ligate-force  /tmp/vR10W27JBX/concat.5.a.bcf /tmp/vR10W27JBX/concat.5.b.bcf /tmp/vR10W27JBX/concat.5.c.bcf
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -l --ligate-force  /tmp/vR10W27JBX/concat.5.a.bcf /tmp/vR10W27JBX/concat.5.b.bcf /tmp/vR10W27JBX/concat.5.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -G -a -D  /tmp/vR10W27JBX/concat.5.a.vcf.gz /tmp/vR10W27JBX/concat.5.b.vcf.gz /tmp/vR10W27JBX/concat.5.c.vcf.gz
657s .. ok
657s 
657s test_vcf_concat:
657s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -G -a -D  /tmp/vR10W27JBX/concat.5.a.vcf.gz /tmp/vR10W27JBX/concat.5.b.vcf.gz /tmp/vR10W27JBX/concat.5.c.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
657s .. ok
657s 
658s test_vcf_concat:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat --no-version -G -a -D  /tmp/vR10W27JBX/concat.5.a.bcf /tmp/vR10W27JBX/concat.5.b.bcf /tmp/vR10W27JBX/concat.5.c.bcf
658s .. ok
658s 
658s test_vcf_concat:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools concat -Ob -G -a -D  /tmp/vR10W27JBX/concat.5.a.bcf /tmp/vR10W27JBX/concat.5.b.bcf /tmp/vR10W27JBX/concat.5.c.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.hdr /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.hdr | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.hdr /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.hdr | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.hdr /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.hdr | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples2 /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples2 /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples2 /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples2 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples3 /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples3 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples3 /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples3 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples3 /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples3 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples4 /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples4 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples4 /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples4 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples4 /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/reheader.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -s /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.samples4 | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.empty.hdr /tmp/autopkgtest.M9R37K/build.dgl/src/test/empty.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/autopkgtest.M9R37K/build.dgl/src/test/empty.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.empty.hdr | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.empty.hdr /tmp/vR10W27JBX/empty.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/empty.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.empty.hdr | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.empty.hdr /tmp/vR10W27JBX/empty.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
658s .. ok
658s 
658s test_vcf_reheader:
658s 	cat /tmp/vR10W27JBX/empty.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.empty.hdr | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.fai /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.fai /tmp/vR10W27JBX/reheader.2.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.fai /tmp/vR10W27JBX/reheader.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.2.hdr -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.fai /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.2.hdr -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.fai /tmp/vR10W27JBX/reheader.2.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -h /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.2.hdr -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.fai /tmp/vR10W27JBX/reheader.2.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.3.fai /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.3.fai /tmp/vR10W27JBX/reheader.3.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_vcf_reheader:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools reheader -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/reheader.3.fai /tmp/vR10W27JBX/reheader.3.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view --no-version
659s .. ok
659s 
659s test_rename_chrs:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate --rename-chrs /tmp/vR10W27JBX/rename.map -Ov /tmp/vR10W27JBX/annotate.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM\t%POS\n'
659s .. ok
659s 
659s test_rename_chrs:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate --rename-chrs /tmp/vR10W27JBX/rename.map -Ob /tmp/vR10W27JBX/annotate.bcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM\t%POS\n'
659s .. ok
659s 
659s test_rename_chrs:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate --rename-chrs /tmp/vR10W27JBX/rename.map -Ov /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM\t%POS\n'
659s .. ok
659s 
659s test_rename_chrs:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools annotate --rename-chrs /tmp/vR10W27JBX/rename.map -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/annotate.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%CHROM\t%POS\n'
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. /tmp/vR10W27JBX/convert.vcf.gz
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,.
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --vcf-ids /tmp/vR10W27JBX/convert.vcf.gz
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --vcf-ids
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --vcf-ids --3N6 /tmp/vR10W27JBX/convert.vcf.gz
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --vcf-ids --3N6
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- /tmp/vR10W27JBX/convert.vcf.gz
659s .. ok
659s 
659s test_vcf_convert:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,-
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert  --vcf-ids -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert  --vcf-ids -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --3N6 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.3N6.gen,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --3N6 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.3N6.gen,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples | grep -v ^##
659s .. ok
659s 
659s test_vcf_convert_hs2vcf:
659s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --vcf-ids -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_hs2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_hs2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.ids.gen.rev,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.gs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --tag PL /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --tag PL
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --tag PL /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --tag PL
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --vcf-ids /tmp/vR10W27JBX/check.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --vcf-ids
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --vcf-ids /tmp/vR10W27JBX/check.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --vcf-ids
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --3N6 /tmp/vR10W27JBX/check.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --3N6
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --3N6 /tmp/vR10W27JBX/check.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --3N6
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --3N6 --vcf-ids /tmp/vR10W27JBX/check.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g -,. --3N6 --vcf-ids
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --3N6 --vcf-ids /tmp/vR10W27JBX/check.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/check.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -g .,- --3N6 --vcf-ids
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h -,.,. /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h -,.,.
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h .,-,. /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h .,-,.
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h .,-,. --vcf-ids /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h .,-,. --vcf-ids
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h .,.,- /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -h .,.,-
660s .. ok
660s 
660s test_vcf_convert_hls2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -H /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hls.gt.hap,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hls.gt.legend,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hls.gt.samples | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_hls2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -H /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hls.gt.hap,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hls.gt.legend,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hls.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --haplegendsample -,.,. /tmp/vR10W27JBX/convert.hap-missing.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.hap-missing.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --haplegendsample -,.,.
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample -,. /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample -,.
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample -,. --vcf-ids /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample -,. --vcf-ids
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample .,- /tmp/vR10W27JBX/convert.vcf.gz
660s .. ok
660s 
660s test_vcf_convert:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample .,-
660s .. ok
660s 
660s test_vcf_convert_hs2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.hap,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.samples | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_hs2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --hapsample2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.hap,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_hs2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --vcf-ids --hapsample2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.ids.hap,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.samples | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_hs2vcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --vcf-ids --hapsample2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.ids.hap,/tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.hs.gt.samples -Ou | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##
660s .. ok
660s 
660s test_vcf_convert_gvcf:
660s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa /tmp/vR10W27JBX/convert.gvcf.vcf.gz
661s .. ok
661s 
661s test_vcf_convert_gvcf:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view -Ob /tmp/vR10W27JBX/convert.gvcf.vcf.gz | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/gvcf.fa | grep -v ^##bcftools
661s .. ok
661s 
661s test_vcf_convert_tsv2vcf:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --no-version  -c ID,CHROM,POS,AA -s SAMPLE1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.23andme
661s .. ok
661s 
661s test_vcf_convert_tsv2vcf:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -Ou  -c ID,CHROM,POS,AA -s SAMPLE1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.23andme | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
661s .. ok
661s 
661s test_vcf_convert_tsv2vcf:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert --no-version  -c -,CHROM,POS,REF,ALT -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.tsv
661s .. ok
661s 
661s test_vcf_convert_tsv2vcf:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools convert -Ou  -c -,CHROM,POS,REF,ALT -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/23andme.fa --tsv2vcf /tmp/autopkgtest.M9R37K/build.dgl/src/test/convert.tsv | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view | grep -v ^##bcftools_
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab 
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab 
661s .. ok
661s 
661s test_vcf_consensus_chain:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab -c /tmp/vR10W27JBX/consensus.1.chain.new >/dev/null; cat /tmp/vR10W27JBX/consensus.1.chain.new
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab 
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab 
661s .. ok
661s 
661s test_vcf_consensus_chain:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H 1 -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab -c /tmp/vR10W27JBX/consensus.2.chain.new >/dev/null; cat /tmp/vR10W27JBX/consensus.2.chain.new
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -I -s - -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab 
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -I -s - -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab 
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -I -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab --mask-with X -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab --mask-with lc  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -I -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab --mask-with X -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab --mask-with lc  
661s .. ok
661s 
661s test_vcf_consensus_chain:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -I -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.tab -c /tmp/vR10W27JBX/consensus.3.chain.new >/dev/null; cat /tmp/vR10W27JBX/consensus.3.chain.new
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H 1  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H 1  
661s .. ok
661s 
661s test_vcf_consensus_chain:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H 1  -c /tmp/vR10W27JBX/consensus.4.chain.new >/dev/null; cat /tmp/vR10W27JBX/consensus.4.chain.new
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus2.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 1  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus2.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 1  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus2.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 2  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus2.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 2  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/empty.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s -  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/empty.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s -  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus3.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 2 -M "?"  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus3.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 2 -M "?"  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus3.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 2 -M "?" -p xx_  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus3.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -H 2 -M "?" -p xx_  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus4.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -s -  
661s .. ok
661s 
661s test_vcf_consensus:
661s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus4.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -s -  
661s .. ok
661s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus5.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus5.fa --haplotype LA  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus5.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus5.fa --haplotype LA  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus6.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus6.fa -s -  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus6.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus6.fa -s -  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 2  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 2  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 4  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 4  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 2pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 2pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 4pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 4pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 1  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 1  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 3  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 3  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 1pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 1pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 3pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus7.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus7.fa -H 3pIu  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s -  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s -  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a .  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a .  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -i 'ALT!="<DEL>"'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -e 'MinDP>15'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -e 'MinDP>15'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -e 'MinDP<15'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus8.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -a . -e 'MinDP<15'  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.9.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.1.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.9.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.1.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.9.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.2.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.9.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.2.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.10.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.1.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.10.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.1.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.10.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.2.fa -H A  
662s .. ok
662s 
662s test_vcf_consensus:
662s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.10.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.9.2.fa -H A  
662s .. ok
662s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.11.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.11.fa -s smpl  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.11.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.11.fa -s smpl  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.11.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.11.fa -s smpl -a N  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.11.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.11.fa -s smpl -a N  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.12.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.12.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.12.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.12.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.13.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.13.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.13.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.13.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.14.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.14.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.14.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.14.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.12.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.12.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.12.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.12.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv :  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.15.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.15.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.16.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -I  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.16.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -s - -I  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.16.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H I  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.16.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.fa -H I  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.17.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -s - -M N -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.17.bed 
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.17.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus2.fa -s - -M N -m /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.17.bed 
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.18.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.18.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.18.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.18.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.19.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.19.fa -s -   
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.19.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.19.fa -s -   
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa -s -  
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa   
663s .. ok
663s 
663s test_vcf_consensus:
663s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa   
664s .. ok
664s 
664s test_vcf_consensus:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa -M . -s b  
664s .. ok
664s 
664s test_vcf_consensus:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa -M . -s b  
664s .. ok
664s 
664s test_vcf_consensus:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa -M . -s a  
664s .. ok
664s 
664s test_vcf_consensus:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.20.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.20.fa -M . -s a  
664s .. ok
664s 
664s test_vcf_consensus:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.21.vcf.gz -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.21.fa   
664s .. ok
664s 
664s test_vcf_consensus:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools consensus /tmp/vR10W27JBX/consensus.21.bcf    -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/consensus.21.fa   
664s .. ok
664s 
664s test_mpileup:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
664s .. ok
664s 
664s test_mpileup:
664s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
665s .. ok
665s 
665s test_mpileup:
665s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -b /tmp/vR10W27JBX/mpileup.bam.list --no-version | grep -v ^##reference
665s .. ok
665s 
665s test_mpileup:
665s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vR10W27JBX/mpileup.bam.urllist | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
665s .. ok
665s 
665s test_mpileup:
665s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
666s .. ok
666s 
666s test_mpileup:
666s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
666s .. ok
666s 
666s test_mpileup:
666s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -b /tmp/vR10W27JBX/mpileup.cram.list --no-version | grep -v ^##reference
667s .. ok
667s 
667s test_mpileup:
667s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vR10W27JBX/mpileup.cram.urllist | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
667s .. ok
667s 
667s test_mpileup:
667s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
667s .. ok
667s 
667s test_mpileup:
667s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
668s .. ok
668s 
668s test_mpileup:
668s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
668s .. ok
668s 
668s test_mpileup:
668s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
669s .. ok
669s 
669s test_mpileup:
669s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference
669s .. ok
669s 
669s test_mpileup:
669s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
669s .. ok
669s 
669s test_mpileup:
669s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference
670s .. ok
670s 
670s test_mpileup:
670s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
670s .. ok
670s 
670s test_mpileup:
670s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
671s .. ok
671s 
671s test_mpileup:
671s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
671s .. ok
671s 
671s test_mpileup:
671s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
672s .. ok
672s 
672s test_mpileup:
672s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
672s .. ok
672s 
672s test_mpileup:
672s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
672s .. ok
672s 
672s test_mpileup:
672s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
673s .. ok
673s 
673s test_mpileup:
673s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
673s .. ok
673s 
673s test_mpileup:
673s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
674s .. ok
674s 
674s test_mpileup:
674s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
674s .. ok
674s 
674s test_mpileup:
674s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
675s .. ok
675s 
675s test_mpileup:
675s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
675s .. ok
675s 
675s test_mpileup:
675s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
675s .. ok
675s 
675s test_mpileup:
675s 	/tmp/autopkgtest.M9R37K/build.dgl/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.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
676s .. ok
676s 
676s test_mpileup:
676s 	/tmp/autopkgtest.M9R37K/build.dgl/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.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
676s .. ok
676s 
676s test_mpileup:
676s 	/tmp/autopkgtest.M9R37K/build.dgl/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.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
677s .. ok
677s 
677s test_mpileup:
677s 	/tmp/autopkgtest.M9R37K/build.dgl/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.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
677s .. ok
677s 
677s test_mpileup:
677s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
678s .. ok
678s 
678s test_mpileup:
678s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
678s .. ok
678s 
678s test_mpileup:
678s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
678s .. ok
678s 
678s test_mpileup:
678s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
679s .. ok
679s 
679s test_mpileup:
679s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
679s .. ok
679s 
679s test_mpileup:
679s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
679s .. ok
679s 
679s test_mpileup:
679s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
680s .. ok
680s 
680s test_mpileup:
680s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
680s .. ok
680s 
680s test_mpileup:
680s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
681s .. ok
681s 
681s test_mpileup:
681s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
681s .. ok
681s 
681s test_mpileup:
681s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
681s .. ok
681s 
681s test_mpileup:
681s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
682s .. ok
682s 
682s test_mpileup:
682s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
682s .. ok
682s 
682s test_mpileup:
682s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
683s .. ok
683s 
683s test_mpileup:
683s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
683s .. ok
683s 
683s test_mpileup:
683s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -r17:100-150 -S ^/tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
683s .. ok
683s 
683s test_mpileup:
683s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.9.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
684s .. ok
684s 
684s test_mpileup:
684s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.9.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
684s .. ok
684s 
684s test_mpileup:
684s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.9.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
685s .. ok
685s 
685s test_mpileup:
685s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.9.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
685s .. ok
685s 
685s test_mpileup:
685s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.9.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
686s .. ok
686s 
686s test_mpileup:
686s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -S /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.9.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
686s .. ok
686s 
686s test_mpileup:
686s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.10.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
686s .. ok
686s 
686s test_mpileup:
686s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.10.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
687s .. ok
687s 
687s test_mpileup:
687s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.10.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
687s .. ok
687s 
687s test_mpileup:
687s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.10.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
688s .. ok
688s 
688s test_mpileup:
688s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.10.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
688s .. ok
688s 
688s test_mpileup:
688s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t17:100-150 -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.10.samples -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.1.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.2.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
688s .. ok
688s 
688s test_mpileup:
688s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference
689s .. ok
689s 
689s test_mpileup:
689s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
689s .. ok
689s 
689s test_mpileup:
689s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
690s .. ok
690s 
690s test_mpileup:
690s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
690s .. ok
690s 
690s test_mpileup:
690s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
691s .. ok
691s 
691s test_mpileup:
691s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup  -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
691s .. ok
691s 
691s test_mpileup:
691s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
692s .. ok
692s 
692s test_mpileup:
692s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
692s .. ok
692s 
692s test_mpileup:
692s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
693s .. ok
693s 
693s test_mpileup:
693s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
693s .. ok
693s 
693s test_mpileup:
693s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
694s .. ok
694s 
694s test_mpileup:
694s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s HG00102 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
694s .. ok
694s 
694s test_mpileup:
694s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
695s .. ok
695s 
695s test_mpileup:
695s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
695s .. ok
695s 
695s test_mpileup:
695s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
696s .. ok
696s 
696s test_mpileup:
696s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
696s .. ok
696s 
696s test_mpileup:
696s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
696s .. ok
696s 
696s test_mpileup:
696s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -s ^HG99999 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
697s .. ok
697s 
697s test_mpileup:
697s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
697s .. ok
697s 
697s test_mpileup:
697s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
698s .. ok
698s 
698s test_mpileup:
698s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
698s .. ok
698s 
698s test_mpileup:
698s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
699s .. ok
699s 
699s test_mpileup:
699s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
699s .. ok
699s 
699s test_mpileup:
699s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
700s .. ok
700s 
700s test_mpileup:
700s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference
700s .. ok
700s 
700s test_mpileup:
700s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.sam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
701s .. ok
701s 
701s test_mpileup:
701s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
701s .. ok
701s 
701s test_mpileup:
701s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
702s .. ok
702s 
702s test_mpileup:
702s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
702s .. ok
702s 
702s test_mpileup:
702s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -G /tmp/autopkgtest.M9R37K/build.dgl/src/test/mplp.11.rgs -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.ref.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.3.cram /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup.4.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
703s .. ok
703s 
703s test_mpileup:
703s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference
703s .. ok
703s 
703s test_mpileup:
703s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
704s .. ok
704s 
704s test_mpileup:
704s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
704s .. ok
704s 
704s test_mpileup:
704s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
704s .. ok
704s 
704s test_mpileup:
704s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
705s .. ok
705s 
705s test_mpileup:
705s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.1.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
705s .. ok
705s 
705s test_mpileup:
705s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
706s .. ok
706s 
706s test_mpileup:
706s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
706s .. ok
706s 
706s test_mpileup:
706s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
707s .. ok
707s 
707s test_mpileup:
707s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
707s .. ok
707s 
707s test_mpileup:
707s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
707s .. ok
707s 
707s test_mpileup:
707s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
708s .. ok
708s 
708s test_mpileup:
708s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
708s .. ok
708s 
708s test_mpileup:
708s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
709s .. ok
709s 
709s test_mpileup:
709s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
709s .. ok
709s 
709s test_mpileup:
709s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
709s .. ok
709s 
709s test_mpileup:
709s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
710s .. ok
710s 
710s test_mpileup:
710s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/indel-AD.2.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
710s .. ok
710s 
710s test_mpileup:
710s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference
711s .. ok
711s 
711s test_mpileup:
711s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
711s .. ok
711s 
711s test_mpileup:
711s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference
711s .. ok
711s 
711s test_mpileup:
711s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/SCR,FMT/SCR -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.cram | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
712s .. ok
712s 
712s test_mpileup:
712s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
712s .. ok
712s 
712s test_mpileup:
712s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
713s .. ok
713s 
713s test_mpileup:
713s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
713s .. ok
713s 
713s test_mpileup:
713s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
713s .. ok
713s 
713s test_mpileup:
713s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
714s .. ok
714s 
714s test_mpileup:
714s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
714s .. ok
714s 
714s test_mpileup:
714s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference
715s .. ok
715s 
715s test_mpileup:
715s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-SCR.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/mpileup-filter.sam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
715s .. ok
715s 
715s test_mpileup:
715s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.1.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference
715s .. ok
715s 
715s test_mpileup:
715s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.1.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.1.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
716s .. ok
716s 
716s test_mpileup:
716s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.2.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference
716s .. ok
716s 
716s test_mpileup:
716s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.2.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.2.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
717s .. ok
717s 
717s test_mpileup:
717s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.3.fa /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.3.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference
717s .. ok
717s 
717s test_mpileup:
717s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.3.fa -Ob /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.3.1.bam /tmp/autopkgtest.M9R37K/build.dgl/src/test/mpileup/annot-NMBZ.3.2.bam | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.gff3 /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.chr.gff3 /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.2.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.2.gff --ncsq 64 /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.nchr.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq.ychr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
718s .. ok
718s 
718s test_csq_real:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0001/EDUMMY0001.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0001/EDUMMY0001.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0001/starts-with-1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
718s .. ok
718s 
718s test_csq_real:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0001/EDUMMY0001.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0001/EDUMMY0001.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0001/starts-with-1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
718s .. ok
718s 
718s test_csq_real:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0002/EDUMMY0002.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0002/EDUMMY0002.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0002/boundaries.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
718s .. ok
718s 
718s test_csq_real:
718s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0003/EDUMMY0003.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0003/EDUMMY0003.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EDUMMY0003/long-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
718s .. ok
718s 
718s test_csq_real:
718s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EMN908947 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/EMN908947 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSG00000173376/ENSG00000173376.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSG00000173376/ENSG00000173376.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSG00000173376/synon.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
719s .. ok
719s 
719s test_csq_real:
719s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
719s .. ok
719s 
719s test_csq_real:
719s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSMUST00000121418 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
719s .. ok
719s 
719s test_csq_real:
719s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENSMUST00000133836 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
719s .. ok
719s 
719s test_csq_real:
719s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000000000 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/start-lost-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/ENST00000218032.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/ENST00000218032.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000218032/start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000227471/ENST00000227471.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000227471/ENST00000227471.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000230048/ENST00000230048.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000230048/ENST00000230048.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000230048/start-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000256452/ENST00000256452.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000256452/ENST00000256452.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000256452/intron.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000263103-INS/insertions.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000269081/ENST00000269081.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000269081/ENST00000269081.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000271583/ENST00000271583.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000271583/ENST00000271583.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000271583/splice-acceptor.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
719s .. ok
719s 
719s test_csq_real:
719s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000285021/ENST00000285021.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000285021/ENST00000285021.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000294661/ENST00000294661.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000294661/ENST00000294661.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000294661/non-coding-boundary.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000294661/ENST00000294661.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000294661/ENST00000294661.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000294661/non-coding-boundary.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000295641/ENST00000295641.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000295641/ENST00000295641.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000295641/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000295641/ENST00000295641.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000295641/ENST00000295641.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000295641/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000301246/ENST00000301246.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000301246/ENST00000301246.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000301246/15bp-insert.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000303039/ENST00000303039.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000303039/ENST00000303039.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000303039/not-a-stop.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000303039/ENST00000303039.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000303039/ENST00000303039.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000303039/not-a-stop.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249.2/ENST00000318249.2.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249/ENST00000318249.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249/ENST00000318249.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249/start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249/ENST00000318249.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249/ENST00000318249.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000318249/start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000329454/ENST00000329454.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000329454/ENST00000329454.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000329454/boundary-deletion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000329454/ENST00000329454.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000329454/ENST00000329454.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000329454/boundary-deletion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/frame1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/frame1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/frame2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/frame2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/frame3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/frame3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
720s test_csq_real:
720s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
720s .. ok
720s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/ENST00000341065.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
721s .. ok
721s 
721s test_csq_real:
721s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000357367/ENST00000357367.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000357367/ENST00000357367.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000357367/stop-retained.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000360372/ENST00000360372.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000360372/ENST00000360372.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000360372/mnp.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000368801.2/ENST00000368801.2.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000368801.2/start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000368801/ENST00000368801.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000368801/ENST00000368801.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000368801/compound-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000373833/ENST00000373833.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000373833/ENST00000373833.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000373833/boundary-insertion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000373833/ENST00000373833.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000373833/ENST00000373833.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000373833/boundary-insertion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000375992/ENST00000375992.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000375992/ENST00000375992.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000378322/ENST00000378322.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000378322/ENST00000378322.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000378322/end-overlap-tscript.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000378322/ENST00000378322.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000378322/ENST00000378322.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000378322/end-overlap-tscript.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
722s .. ok
722s 
722s test_csq_real:
722s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000379416 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf       | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf       | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf       | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf       | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf                 | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
722s .. ok
722s 
722s test_csq_real:
722s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000381157/ENST00000381157.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000381157/ENST00000381157.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000381157/haploid-diploid.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000382647/ENST00000382647.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000382647/ENST00000382647.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000390520/ENST00000390520.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000390520/ENST00000390520.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000390520/deletion-overlap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000400151/ENST00000400151.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000400151/ENST00000400151.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000400151/long-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000409523/ENST00000409523.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000409523/ENST00000409523.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000409523/long-overlapping-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000410009 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
723s .. ok
723s 
723s test_csq_real:
723s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000410009 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
723s .. ok
723s 
723s test_csq_real:
723s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000410009 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000410009/ENST00000410009.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000410009/ENST00000410009.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000410009/frameshift.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000413103/ENST00000413103.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000413103/ENST00000413103.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000413103/long-deletion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420190/ENST00000420190.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420190/ENST00000420190.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420190/abort-in-csq-push.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420670/ENST00000420670.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420670/ENST00000420670.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420670/segfault.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420670/ENST00000420670.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420670/ENST00000420670.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000420670/start-stop-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000422159 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf  | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/insert3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/insert3.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/snps.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/ENST00000423372.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000423372/snps.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
723s .. ok
723s 
723s test_csq_real:
723s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000436063/ENST00000436063.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000436063/ENST00000436063.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000436063/insert-before-utr.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000448695/ENST00000448695.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000448695/ENST00000448695.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000479739/ENST00000479739.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000479739/ENST00000479739.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000479739/short-cds-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000479739/ENST00000479739.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000479739/ENST00000479739.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000479739/short-cds-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000518414/ENST00000518414.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000518414/ENST00000518414.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000519442/ENST00000519442.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000519442/ENST00000519442.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000519442/synon-splice-region-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520795/ENST00000520795.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520795/ENST00000520795.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520795/long-inside-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520795/ENST00000520795.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520795/ENST00000520795.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520795/long-inside-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520868/ENST00000520868.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520868/ENST00000520868.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000520868/long-deletion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000528237/ENST00000528237.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000528237/ENST00000528237.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000536784/ENST00000536784.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000536784/ENST00000536784.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000536784/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000536784/ENST00000536784.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000536784/ENST00000536784.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000536784/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000542803/ENST00000542803.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000542803/ENST00000542803.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000542803/splice-region.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
724s test_csq_real:
724s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000542803/ENST00000542803.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000542803/ENST00000542803.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000542803/splice-region.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
724s .. ok
724s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000543077/ENST00000543077.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000543077/ENST00000543077.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000543077/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000543077/ENST00000543077.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000543077/ENST00000543077.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000543077/not-a-start-lost.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000545279/ENST00000545279.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000545279/ENST00000545279.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000545279/splice-region-insert.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000557788/ENST00000557788.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000557788/ENST00000557788.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000557788/long-overlap-del.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000571540/ENST00000571540.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000571540/ENST00000571540.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000571540/nmd.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000573314/ENST00000573314.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000573314/ENST00000573314.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -l -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000573314/ENST00000573314.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000573314/ENST00000573314.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	cd /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000580206 && /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf  | ../sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000593942/ENST00000593942.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000593942/ENST00000593942.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000593942/last-codon-deletion.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_csq_real:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools csq -f /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000624631/ENST00000624631.fa -g /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000624631/ENST00000624631.gff /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/ENST00000624631/ambiguous.vcf | /tmp/autopkgtest.M9R37K/build.dgl/src/test/csq/sort-csq | /tmp/autopkgtest.M9R37K/build.dgl/src/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
725s .. ok
725s 
725s test_roh:
725s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^#
726s .. ok
726s 
726s test_roh:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz -Or -G30 --AF-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.tab.gz| grep -v ^#
726s .. ok
726s 
726s test_roh:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz -Or -G30 --AF-file /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.tab.gz --ignore-homref| grep -v ^#
726s .. ok
726s 
726s test_roh:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^#
726s .. ok
726s 
726s test_roh:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^#
726s .. ok
726s 
726s test_roh:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^#
726s .. ok
726s 
726s test_roh:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools roh /tmp/autopkgtest.M9R37K/build.dgl/src/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^#
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u GT,GT /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u GT,PL /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u PL,GT /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u PL,PL /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -p s1,s1 /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 /tmp/vR10W27JBX/gtcheck.2.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0  /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/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/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.M9R37K/build.dgl/src/test/gtcheck.3.pairs /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u PL /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 --n-matches 4 /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO  | sort
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -p B,C,B,D /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u GT,GT -H /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u GT,PL -H /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u PL,GT -H /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -u PL,PL -H /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.M9R37K/build.dgl/src/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/vR10W27JBX/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -e 0 -P /tmp/autopkgtest.M9R37K/build.dgl/src/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/vR10W27JBX/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -u GT -e 30 /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
726s .. ok
726s 
726s test_gtcheck:
726s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -u GT -e 300 /tmp/vR10W27JBX/gtcheck.1.vcf.gz -g /tmp/vR10W27JBX/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -u PL -e 30 /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck  /tmp/vR10W27JBX/gtcheck.ntop.vcf.gz -g /tmp/vR10W27JBX/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck --n-matches 2 /tmp/vR10W27JBX/gtcheck.ntop.vcf.gz -g /tmp/vR10W27JBX/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck  /tmp/vR10W27JBX/gtcheck.5.vcf.gz -g /tmp/vR10W27JBX/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -p A,B,B,C /tmp/vR10W27JBX/gtcheck.6.vcf.gz  | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s test_gtcheck:
727s 	/tmp/autopkgtest.M9R37K/build.dgl/src/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/vR10W27JBX/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
727s .. ok
727s 
727s 
727s Number of tests:
727s     total   .. 1662
727s     passed  .. 1662
727s     failed  .. 0
727s 
727s mv: cannot stat 'bcftools.orig': No such file or directory
727s autopkgtest [19:23:32]: test command1: -----------------------]
732s autopkgtest [19:23:37]: test command1:  - - - - - - - - - - results - - - - - - - - - -
732s command1             PASS
736s autopkgtest [19:23:41]: @@@@@@@@@@@@@@@@@@@@ summary
736s command1             PASS