0s autopkgtest [17:18:36]: starting date and time: 2025-03-15 17:18:36+0000
0s autopkgtest [17:18:36]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
0s autopkgtest [17:18:36]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tfkawbqy/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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade samtools --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.201 lxd-armhf-10.145.243.201:autopkgtest/ubuntu/plucky/armhf
20s autopkgtest [17:18:56]: testbed dpkg architecture: armhf
22s autopkgtest [17:18:58]: testbed apt version: 2.9.33
25s autopkgtest [17:19:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup
27s autopkgtest [17:19:03]: testbed release detected to be: None
35s autopkgtest [17:19:11]: updating testbed package index (apt update)
37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB]
37s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
38s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
38s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB]
38s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B]
38s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B]
38s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB]
38s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB]
38s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B]
38s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B]
38s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB]
54s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB]
55s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB]
56s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB]
57s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB]
69s Get:20 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB]
71s Fetched 40.7 MB in 34s (1212 kB/s)
72s Reading package lists...
77s autopkgtest [17:19:53]: upgrading testbed (apt dist-upgrade and autopurge)
79s Reading package lists...
80s Building dependency tree...
80s Reading state information...
81s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
82s Starting 2 pkgProblemResolver with broken count: 0
82s Done
84s Entering ResolveByKeep
85s
85s Calculating upgrade...
86s The following packages will be upgraded:
86s libc-bin libc6 locales pinentry-curses sos
87s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
87s Need to get 8128 kB of archives.
87s After this operation, 0 B of additional disk space will be used.
87s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB]
90s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB]
90s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB]
94s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB]
94s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB]
95s Preconfiguring packages ...
95s Fetched 8128 kB in 8s (1048 kB/s)
95s (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 64655 files and directories currently installed.)
95s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ...
95s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
96s Setting up libc6:armhf (2.41-1ubuntu2) ...
96s (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 64655 files and directories currently installed.)
96s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ...
96s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
96s Setting up libc-bin (2.41-1ubuntu2) ...
97s (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 64655 files and directories currently installed.)
97s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
97s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
97s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ...
98s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
98s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ...
98s Unpacking sos (4.9.0-5) over (4.9.0-4) ...
98s Setting up sos (4.9.0-5) ...
99s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
99s Setting up locales (2.41-1ubuntu2) ...
100s Generating locales (this might take a while)...
102s en_US.UTF-8... done
102s Generation complete.
102s Processing triggers for systemd (257.3-1ubuntu3) ...
103s Processing triggers for man-db (2.13.0-1) ...
107s Reading package lists...
107s Building dependency tree...
107s Reading state information...
108s Starting pkgProblemResolver with broken count: 0
108s Starting 2 pkgProblemResolver with broken count: 0
108s Done
108s Solving dependencies...
109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
111s autopkgtest [17:20:27]: rebooting testbed after setup commands that affected boot
152s autopkgtest [17:21:08]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2
176s autopkgtest [17:21:32]: @@@@@@@@@@@@@@@@@@@@ apt-source samtools
197s Get:1 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (dsc) [2281 B]
197s Get:2 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (tar) [5683 kB]
197s Get:3 http://ftpmaster.internal/ubuntu plucky/universe samtools 1.21-1 (diff) [22.1 kB]
197s gpgv: Signature made Thu Feb 6 21:19:50 2025 UTC
197s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
197s gpgv: issuer "emollier@debian.org"
197s gpgv: Can't check signature: No public key
197s dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-1.dsc: no acceptable signature found
197s autopkgtest [17:21:53]: testing package samtools version 1.21-1
199s autopkgtest [17:21:55]: build not needed
203s autopkgtest [17:21:59]: test run-unit-test: preparing testbed
205s Reading package lists...
205s Building dependency tree...
205s Reading state information...
206s Starting pkgProblemResolver with broken count: 0
206s Starting 2 pkgProblemResolver with broken count: 0
206s Done
207s The following NEW packages will be installed:
207s libdeflate0 libhts3t64 libhtscodecs2 samtools samtools-test tabix
207s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
207s Need to get 3970 kB of archives.
207s After this operation, 22.0 MB of additional disk space will be used.
207s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB]
207s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB]
207s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB]
208s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.21-1 [619 kB]
208s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools-test all 1.21-1 [2413 kB]
211s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.21+ds-1 [433 kB]
212s Fetched 3970 kB in 5s (868 kB/s)
212s Selecting previously unselected package libdeflate0:armhf.
212s (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 64655 files and directories currently installed.)
212s Preparing to unpack .../0-libdeflate0_1.23-1_armhf.deb ...
212s Unpacking libdeflate0:armhf (1.23-1) ...
212s Selecting previously unselected package libhtscodecs2:armhf.
212s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_armhf.deb ...
212s Unpacking libhtscodecs2:armhf (1.6.1-2) ...
212s Selecting previously unselected package libhts3t64:armhf.
212s Preparing to unpack .../2-libhts3t64_1.21+ds-1_armhf.deb ...
212s Unpacking libhts3t64:armhf (1.21+ds-1) ...
212s Selecting previously unselected package samtools.
212s Preparing to unpack .../3-samtools_1.21-1_armhf.deb ...
212s Unpacking samtools (1.21-1) ...
212s Selecting previously unselected package samtools-test.
212s Preparing to unpack .../4-samtools-test_1.21-1_all.deb ...
212s Unpacking samtools-test (1.21-1) ...
212s Selecting previously unselected package tabix.
212s Preparing to unpack .../5-tabix_1.21+ds-1_armhf.deb ...
212s Unpacking tabix (1.21+ds-1) ...
212s Setting up libhtscodecs2:armhf (1.6.1-2) ...
212s Setting up libdeflate0:armhf (1.23-1) ...
212s Setting up libhts3t64:armhf (1.21+ds-1) ...
212s Setting up samtools-test (1.21-1) ...
212s Setting up tabix (1.21+ds-1) ...
212s Setting up samtools (1.21-1) ...
212s Processing triggers for man-db (2.13.0-1) ...
213s Processing triggers for libc-bin (2.41-1ubuntu2) ...
227s autopkgtest [17:22:23]: test run-unit-test: [-----------------------
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -e test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s test_reference:
230s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
230s .. ok
230s
230s bgzip -c -b 65272 -s 5 /tmp/mTCQSioAb_/bgzip.dat.gz
230s .. ok
230s
230s bgzip -c -b 979200 -s 6 /tmp/mTCQSioAb_/bgzip.dat.gz
230s .. ok
230s
230s bgzip -c -b 652804 -s 6 /tmp/mTCQSioAb_/bgzip.dat.gz
230s .. ok
230s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa 3:11-13 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa.gz 3:11-13 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa 2:998-1003 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa.gz 2:998-1003 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa 1:100-104 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa.gz 1:100-104 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa 1:99998-100007 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools faidx /tmp/mTCQSioAb_/faidx.fa.gz 1:99998-100007 | grep -v '^>'
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq 3:11-13
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq.gz 3:11-13
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq 2:998-1003
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq.gz 2:998-1003
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq 1:100-104
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq.gz 1:100-104
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq 1:99998-100007
231s .. ok
231s
231s .. ok
231s
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fqidx /tmp/mTCQSioAb_/fqidx.fq.gz 1:99998-100007
231s .. ok
231s
231s .. ok
231s
231s test_dict:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/dict.fa
231s .. ok
231s
231s test_dict:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/mTCQSioAb_/dict.fa.gz
231s .. ok
231s
231s test_dict:
231s cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/dict.fa | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
231s .. ok
231s
231s test_dict:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools dict -AH < /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/dict.alias.fa
231s .. ok
231s
231s test_dict:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools dict -H -l /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/dict.alt < /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/dict.alias.fa
231s .. ok
231s
231s test_index:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view /tmp/mTCQSioAb_/large_chrom.bam ref2
231s .. ok
231s
231s test_index:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view /tmp/mTCQSioAb_/large_chrom.bam ref2:1-541556283
231s .. ok
231s
231s test_index:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai
231s .. ok
231s
231s test_index:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/mTCQSioAb_/test_input_1_b.bam.bai ref2
231s .. ok
231s
231s test_index:
231s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/mTCQSioAb_/test_input_1_b.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -O sam - -X -cp -R ref2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/mTCQSioAb_/test_input_1_b.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/mTCQSioAb_/test_input_1_b_opt.bam.bai ref2
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/mTCQSioAb_/auto_indexed.csi && cat /tmp/mTCQSioAb_/auto_indexed.csi
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/mTCQSioAb_/auto_indexed.crai && cat /tmp/mTCQSioAb_/auto_indexed.crai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -c /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/mTCQSioAb_/auto_indexed.csi && cat /tmp/mTCQSioAb_/auto_indexed.csi
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -@ 2 /tmp/mTCQSioAb_/large_chrom.bam ref2
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -@ 2 /tmp/mTCQSioAb_/large_chrom.bam ref2:1-541556283
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam && cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/mTCQSioAb_/test_input_1_b.bam.bai ref2
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/mTCQSioAb_/test_input_1_b.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -O sam - -X -cp -R ref2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai /tmp/mTCQSioAb_/test_input_1_b.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/mTCQSioAb_/test_input_1_b_opt.bam.bai ref2
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -@ 2 -M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam && cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam.bai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -@ 2 -X /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam.bai ref2
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam /tmp/mTCQSioAb_/auto_indexed.csi && cat /tmp/mTCQSioAb_/auto_indexed.csi
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -@ 2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.cram /tmp/mTCQSioAb_/auto_indexed.crai && cat /tmp/mTCQSioAb_/auto_indexed.crai
232s .. ok
232s
232s test_index:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools index -@ 2 -c /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.sam /tmp/mTCQSioAb_/auto_indexed.csi && cat /tmp/mTCQSioAb_/auto_indexed.csi
232s .. ok
232s
232s test_mpileup:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup -b /tmp/mTCQSioAb_/mpileup.bam.list -f /tmp/mTCQSioAb_/mpileup.ref.fa.gz -r17:100-150
232s .. ok
232s
232s test_mpileup:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup -b /tmp/mTCQSioAb_/mpileup.cram.list -f /tmp/mTCQSioAb_/mpileup.ref.fa.gz -r17:100-150
232s .. ok
232s
232s test_mpileup:
232s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup -b /tmp/mTCQSioAb_/mpileup.bam.urllist -f /tmp/mTCQSioAb_/mpileup.ref.fa.gz -r17:100-150
233s .. ok
233s
233s test_mpileup:
233s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup -b /tmp/mTCQSioAb_/mpileup.cram.urllist -f /tmp/mTCQSioAb_/mpileup.ref.fa.gz -r17:100-150
233s .. ok
233s
233s test_mpileup:
233s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/mTCQSioAb_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mTCQSioAb_/mpileup.1.bam | grep -v mpileup
233s .. ok
233s
233s test_mpileup:
233s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup -B --ff 0x14 -f /tmp/mTCQSioAb_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mTCQSioAb_/mpileup.1.cram | grep -v mpileup
233s .. ok
233s
233s test_mpileup:
233s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools mpileup /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/mpileup/overlap.bam | grep 128814202
233s ./test/test.pl: no IO::Pty module or can't open pty; skipping usage tests
233s .. ok
233s
233s test_usage:
233s samtools
233s test_view:
234s Generating test data file .................. done
234s 1: SAM -> BAM -> SAM .. ok
234s
234s 2: SAM -> uncompressed BAM .. ok
234s
234s 3: uncompressed BAM -> SAM and compare .. ok
234s
234s 4: SAM -> fast compressed BAM .. ok
234s
234s 5: fast compressed BAM -> SAM and compare .. ok
234s
235s 6: SAM -> CRAM -> SAM (UR header tags) .. ok
235s
235s 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
235s
235s 8: BAM -> CRAM with UR -> SAM .. ok
235s
236s 9: SAM -> BAM (M5 header tags) .. ok
236s
236s 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
236s
236s 11: CRAM -> BAM with UR .. ok
236s
236s 12: CRAM -> BAM with M5 .. ok
236s
236s 13: SAM -> SAM via stdout .. ok
236s
236s 14: SAM -> BAM via stdout .. ok
236s
237s 15: SAM -> CRAM via stdout .. ok
237s
237s 16: SAM from stdin -> SAM .. ok
237s
237s 17: BAM from stdin -> SAM .. ok
237s
237s 18: CRAM from stdin -> SAM .. ok
237s
237s 19: samtools view -H (SAM input) .. ok
237s
237s 20: samtools view -H (BAM input) .. ok
237s
237s 21: samtools view -H (CRAM input) .. ok
237s
237s 22: No headers (SAM input) .. ok
237s
237s 23: No headers (BAM input) .. ok
237s
238s 24: No headers (CRAM input) .. ok
238s
238s 25: Filter -f 128 (SAM input) .. ok
238s
238s 26: Count -f 128 (SAM input) .. ok
238s
238s 27: Filter -f 128 (BAM input) .. ok
238s
238s 28: Count -f 128 (BAM input) .. ok
238s
238s 29: Filter -f 128 (CRAM input) .. ok
238s
238s 30: Count -f 128 (CRAM input) .. ok
238s
238s 31: Filter -F 128 (SAM input) .. ok
238s
238s 32: Count -F 128 (SAM input) .. ok
238s
238s 33: Filter -F 128 (BAM input) .. ok
238s
238s 34: Count -F 128 (BAM input) .. ok
238s
239s 35: Filter -F 128 (CRAM input) .. ok
239s
239s 36: Count -F 128 (CRAM input) .. ok
239s
239s 37: Filter -F 128 -f 2 (SAM input) .. ok
239s
239s 38: Count -F 128 -f 2 (SAM input) .. ok
239s
239s 39: Filter -F 128 -f 2 (BAM input) .. ok
239s
239s 40: Count -F 128 -f 2 (BAM input) .. ok
239s
239s 41: Filter -F 128 -f 2 (CRAM input) .. ok
239s
239s 42: Count -F 128 -f 2 (CRAM input) .. ok
239s
239s 43: Filter -r grp2 (SAM input) .. ok
239s
239s 44: Count -r grp2 (SAM input) .. ok
239s
239s 45: Filter -r grp2 (BAM input) .. ok
239s
239s 46: Count -r grp2 (BAM input) .. ok
239s
240s 47: Filter -r grp2 (CRAM input) .. ok
240s
240s 48: Count -r grp2 (CRAM input) .. ok
240s
240s 49: Filter -R /tmp/mTCQSioAb_/view.001.fogn (SAM input) .. ok
240s
240s 50: Count -R /tmp/mTCQSioAb_/view.001.fogn (SAM input) .. ok
240s
240s 51: Filter -R /tmp/mTCQSioAb_/view.001.fogn (BAM input) .. ok
240s
240s 52: Count -R /tmp/mTCQSioAb_/view.001.fogn (BAM input) .. ok
240s
240s 53: Filter -R /tmp/mTCQSioAb_/view.001.fogn (CRAM input) .. ok
240s
240s 54: Count -R /tmp/mTCQSioAb_/view.001.fogn (CRAM input) .. ok
240s
240s 55: Filter -R /tmp/mTCQSioAb_/view.001.fogn -r grp2 (SAM input).. ok
240s
240s 56: Count -R /tmp/mTCQSioAb_/view.001.fogn -r grp2 (SAM input).. ok
240s
240s 57: Filter -R /tmp/mTCQSioAb_/view.001.fogn -r grp2 (BAM input).. ok
240s
240s 58: Count -R /tmp/mTCQSioAb_/view.001.fogn -r grp2 (BAM input).. ok
240s
240s 59: Filter -R /tmp/mTCQSioAb_/view.001.fogn -r grp2 (CRAM input).. ok
240s
240s 60: Count -R /tmp/mTCQSioAb_/view.001.fogn -r grp2 (CRAM input).. ok
240s
241s 61: Filter -r grp2 -R /tmp/mTCQSioAb_/view.001.fogn (SAM input).. ok
241s
241s 62: Count -r grp2 -R /tmp/mTCQSioAb_/view.001.fogn (SAM input).. ok
241s
241s 63: Filter -r grp2 -R /tmp/mTCQSioAb_/view.001.fogn (BAM input).. ok
241s
241s 64: Count -r grp2 -R /tmp/mTCQSioAb_/view.001.fogn (BAM input).. ok
241s
241s 65: Filter -r grp2 -R /tmp/mTCQSioAb_/view.001.fogn (CRAM input).. ok
241s
241s 66: Count -r grp2 -R /tmp/mTCQSioAb_/view.001.fogn (CRAM input).. ok
241s
241s 67: Filter -N /tmp/mTCQSioAb_/view.001.forn (SAM input) .. ok
241s
241s 68: Count -N /tmp/mTCQSioAb_/view.001.forn (SAM input) .. ok
241s
241s 69: Filter -N /tmp/mTCQSioAb_/view.001.forn (BAM input) .. ok
241s
241s 70: Count -N /tmp/mTCQSioAb_/view.001.forn (BAM input) .. ok
241s
241s 71: Filter -N /tmp/mTCQSioAb_/view.001.forn (CRAM input) .. ok
241s
241s 72: Count -N /tmp/mTCQSioAb_/view.001.forn (CRAM input) .. ok
241s
241s 73: Filter -d BC (SAM input) .. ok
241s
241s 74: Count -d BC (SAM input) .. ok
241s
241s 75: Filter -d BC (BAM input) .. ok
241s
241s 76: Count -d BC (BAM input) .. ok
241s
242s 77: Filter -d BC (CRAM input) .. ok
242s
242s 78: Count -d BC (CRAM input) .. ok
242s
242s 79: Filter -d BC:TGCA (SAM input) .. ok
242s
242s 80: Count -d BC:TGCA (SAM input) .. ok
242s
242s 81: Filter -d BC:TGCA (BAM input) .. ok
242s
242s 82: Count -d BC:TGCA (BAM input) .. ok
242s
242s 83: Filter -d BC:TGCA (CRAM input) .. ok
242s
242s 84: Count -d BC:TGCA (CRAM input) .. ok
242s
242s 85: Filter -D BC:/tmp/mTCQSioAb_/view.001.fobc (SAM input) .. ok
242s
242s 86: Count -D BC:/tmp/mTCQSioAb_/view.001.fobc (SAM input) .. ok
242s
242s 87: Filter -D BC:/tmp/mTCQSioAb_/view.001.fobc (BAM input) .. ok
242s
242s 88: Count -D BC:/tmp/mTCQSioAb_/view.001.fobc (BAM input) .. ok
242s
243s 89: Filter -D BC:/tmp/mTCQSioAb_/view.001.fobc (CRAM input) .. ok
243s
243s 90: Count -D BC:/tmp/mTCQSioAb_/view.001.fobc (CRAM input) .. ok
243s
243s 91: Filter -D BC:/tmp/mTCQSioAb_/view.001.fobc -d BC:TGCA (SAM input).. ok
243s
243s 92: Count -D BC:/tmp/mTCQSioAb_/view.001.fobc -d BC:TGCA (SAM input).. ok
243s
243s 93: Filter -D BC:/tmp/mTCQSioAb_/view.001.fobc -d BC:TGCA (BAM input).. ok
243s
243s 94: Count -D BC:/tmp/mTCQSioAb_/view.001.fobc -d BC:TGCA (BAM input).. ok
243s
243s 95: Filter -D BC:/tmp/mTCQSioAb_/view.001.fobc -d BC:TGCA (CRAM input).. ok
243s
243s 96: Count -D BC:/tmp/mTCQSioAb_/view.001.fobc -d BC:TGCA (CRAM input).. ok
243s
243s 97: Filter -d BC:TGCA -D BC:/tmp/mTCQSioAb_/view.001.fobc (SAM input).. ok
243s
243s 98: Count -d BC:TGCA -D BC:/tmp/mTCQSioAb_/view.001.fobc (SAM input).. ok
243s
243s 99: Filter -d BC:TGCA -D BC:/tmp/mTCQSioAb_/view.001.fobc (BAM input).. ok
243s
243s 100: Count -d BC:TGCA -D BC:/tmp/mTCQSioAb_/view.001.fobc (BAM input).. ok
243s
243s 101: Filter -d BC:TGCA -D BC:/tmp/mTCQSioAb_/view.001.fobc (CRAM input).. ok
243s
243s 102: Count -d BC:TGCA -D BC:/tmp/mTCQSioAb_/view.001.fobc (CRAM input).. ok
243s
243s 103: Filter -D RG:/tmp/mTCQSioAb_/view.001.fogn (SAM input) .. ok
243s
243s 104: Count -D RG:/tmp/mTCQSioAb_/view.001.fogn (SAM input) .. ok
243s
243s 105: Filter -D RG:/tmp/mTCQSioAb_/view.001.fogn (BAM input) .. ok
243s
243s 106: Count -D RG:/tmp/mTCQSioAb_/view.001.fogn (BAM input) .. ok
243s
244s 107: Filter -D RG:/tmp/mTCQSioAb_/view.001.fogn (CRAM input).. ok
244s
244s 108: Count -D RG:/tmp/mTCQSioAb_/view.001.fogn (CRAM input) .. ok
244s
244s 109: Filter -d NE:TGCA (SAM input) .. ok
244s
244s 110: Count -d NE:TGCA (SAM input) .. ok
244s
244s 111: Filter -d NE:TGCA (BAM input) .. ok
244s
244s 112: Count -d NE:TGCA (BAM input) .. ok
244s
244s 113: Filter -d NE:TGCA (CRAM input) .. ok
244s
244s 114: Count -d NE:TGCA (CRAM input) .. ok
244s
244s 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test115.sam -h -d TGCA /tmp/mTCQSioAb_/view.001.sam --no-PG
244s
244s
244s .. expected failure
244s
244s 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -d TGCA /tmp/mTCQSioAb_/view.001.sam --no-PG
244s
244s
244s .. expected failure
244s
244s 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test117.sam -h -d TGCA /tmp/mTCQSioAb_/view.test001.bam --no-PG
244s
244s
244s .. expected failure
244s
244s 118: Count -d TGCA (BAM input) Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -d TGCA /tmp/mTCQSioAb_/view.test001.bam --no-PG
244s
244s
244s .. expected failure
244s
244s 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
244s samtools view: Invalid "tag:value" option: "TGCA"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test119.sam -h -d TGCA /tmp/mTCQSioAb_/view.test006.cram --no-PG
244s
244s
244s .. expected failure
244s
244s 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -d TGCA /tmp/mTCQSioAb_/view.test006.cram --no-PG
244s
244s
244s .. expected failure
244s
244s 121: Filter -D BClong:/tmp/mTCQSioAb_/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mTCQSioAb_/view.001.fobc"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test121.sam -h -D BClong:/tmp/mTCQSioAb_/view.001.fobc /tmp/mTCQSioAb_/view.001.sam --no-PG
244s
244s
244s .. expected failure
244s
244s 122: Count -D BClong:/tmp/mTCQSioAb_/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mTCQSioAb_/view.001.fobc"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -D BClong:/tmp/mTCQSioAb_/view.001.fobc /tmp/mTCQSioAb_/view.001.sam --no-PG
244s
244s
244s .. expected failure
244s
244s 123: Filter -D BClong:/tmp/mTCQSioAb_/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mTCQSioAb_/view.001.fobc"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test123.sam -h -D BClong:/tmp/mTCQSioAb_/view.001.fobc /tmp/mTCQSioAb_/view.test001.bam --no-PG
244s
244s
244s .. expected failure
244s
244s 124: Count -D BClong:/tmp/mTCQSioAb_/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mTCQSioAb_/view.001.fobc"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -D BClong:/tmp/mTCQSioAb_/view.001.fobc /tmp/mTCQSioAb_/view.test001.bam --no-PG
244s
244s
244s .. expected failure
244s
244s 125: Filter -D BClong:/tmp/mTCQSioAb_/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mTCQSioAb_/view.001.fobc"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test125.sam -h -D BClong:/tmp/mTCQSioAb_/view.001.fobc /tmp/mTCQSioAb_/view.test006.cram --no-PG
244s
244s
244s .. expected failure
244s
244s 126: Count -D BClong:/tmp/mTCQSioAb_/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/mTCQSioAb_/view.001.fobc"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -D BClong:/tmp/mTCQSioAb_/view.001.fobc /tmp/mTCQSioAb_/view.test006.cram --no-PG
244s
244s
244s .. expected failure
244s
244s 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/mTCQSioAb_/view.001.sam --no-PG
244s
244s
244s .. expected failure
244s
244s 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mTCQSioAb_/view.001.sam --no-PG
244s
244s
244s .. expected failure
244s
244s 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/mTCQSioAb_/view.test001.bam --no-PG
244s
244s
244s .. expected failure
244s
244s 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mTCQSioAb_/view.test001.bam --no-PG
244s
244s
244s .. expected failure
244s
244s 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -o /tmp/mTCQSioAb_/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/mTCQSioAb_/view.test006.cram --no-PG
244s
244s
244s .. expected failure
244s
244s 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
244s Failed command:
244s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/mTCQSioAb_/view.test006.cram --no-PG
244s
244s
244s .. expected failure
244s
244s 133: Filter -d NM:13 (SAM input) .. ok
244s
244s 134: Count -d NM:13 (SAM input) .. ok
244s
244s 135: Filter -d NM:13 (BAM input) .. ok
244s
244s 136: Count -d NM:13 (BAM input) .. ok
244s
245s 137: Filter -d NM:13 (CRAM input) .. ok
245s
245s 138: Count -d NM:13 (CRAM input) .. ok
245s
245s 139: Filter -d ab:z (SAM input) .. ok
245s
245s 140: Count -d ab:z (SAM input) .. ok
245s
245s 141: Filter -d ab:z (BAM input) .. ok
245s
245s 142: Count -d ab:z (BAM input) .. ok
245s
246s 143: Filter -d ab:z (CRAM input) .. ok
246s
246s 144: Count -d ab:z (CRAM input) .. ok
246s
246s 145: Filter -l Library 2 (SAM input) .. ok
246s
246s 146: Count -l Library 2 (SAM input) .. ok
246s
246s 147: Filter -l Library 2 (BAM input) .. ok
246s
246s 148: Count -l Library 2 (BAM input) .. ok
246s
246s 149: Filter -l Library 2 (CRAM input) .. ok
246s
246s 150: Count -l Library 2 (CRAM input) .. ok
246s
246s 151: Filter -l Library 3 (SAM input) .. ok
246s
246s 152: Count -l Library 3 (SAM input) .. ok
246s
246s 153: Filter -l Library 3 (BAM input) .. ok
246s
246s 154: Count -l Library 3 (BAM input) .. ok
246s
246s 155: Filter -l Library 3 (CRAM input) .. ok
246s
247s 156: Count -l Library 3 (CRAM input) .. ok
247s
247s 157: Filter -q 50 (SAM input) .. ok
247s
247s 158: Count -q 50 (SAM input) .. ok
247s
247s 159: Filter -q 50 (BAM input) .. ok
247s
247s 160: Count -q 50 (BAM input) .. ok
247s
247s 161: Filter -q 50 (CRAM input) .. ok
247s
247s 162: Count -q 50 (CRAM input) .. ok
247s
247s 163: Filter -q 99 (SAM input) .. ok
247s
247s 164: Count -q 99 (SAM input) .. ok
247s
247s 165: Filter -q 99 (BAM input) .. ok
247s
247s 166: Count -q 99 (BAM input) .. ok
247s
247s 167: Filter -q 99 (CRAM input) .. ok
247s
247s 168: Count -q 99 (CRAM input) .. ok
247s
247s 169: Filter -q 100 (SAM input) .. ok
247s
247s 170: Count -q 100 (SAM input) .. ok
247s
247s 171: Filter -q 100 (BAM input) .. ok
247s
247s 172: Count -q 100 (BAM input) .. ok
247s
248s 173: Filter -q 100 (CRAM input) .. ok
248s
248s 174: Count -q 100 (CRAM input) .. ok
248s
248s 175: Filter -x fa (SAM input) .. ok
248s
248s 176: Count -x fa (SAM input) .. ok
248s
248s 177: Filter -x fa (BAM input) .. ok
248s
248s 178: Count -x fa (BAM input) .. ok
248s
248s 179: Filter -x fa (CRAM input) .. ok
248s
248s 180: Count -x fa (CRAM input) .. ok
248s
248s 181: Filter -x fa -x ha (SAM input) .. ok
248s
248s 182: Count -x fa -x ha (SAM input) .. ok
248s
248s 183: Filter -x fa -x ha (BAM input) .. ok
248s
248s 184: Count -x fa -x ha (BAM input) .. ok
248s
249s 185: Filter -x fa -x ha (CRAM input) .. ok
249s
249s 186: Count -x fa -x ha (CRAM input) .. ok
249s
249s 187: Filter -x fa,ha (SAM input) .. ok
249s
249s 188: Count -x fa,ha (SAM input) .. ok
249s
249s 189: Filter -x fa,ha (BAM input) .. ok
249s
249s 190: Count -x fa,ha (BAM input) .. ok
249s
249s 191: Filter -x fa,ha (CRAM input) .. ok
249s
249s 192: Count -x fa,ha (CRAM input) .. ok
249s
249s 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
249s
249s 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
249s
249s 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
249s
249s 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
249s
249s 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
249s
249s 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
249s
249s 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
249s
250s 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
250s
250s 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
250s
250s 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
250s
250s 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
250s
250s 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
250s
250s 205: Filter -x fa -r grp2 (SAM input) .. ok
250s
250s 206: Count -x fa -r grp2 (SAM input) .. ok
250s
250s 207: Filter -x fa -r grp2 (BAM input) .. ok
250s
250s 208: Count -x fa -r grp2 (BAM input) .. ok
250s
250s 209: Filter -x fa -r grp2 (CRAM input) .. ok
250s
250s 210: Count -x fa -r grp2 (CRAM input) .. ok
250s
250s 211: Filter -x RG -r grp2 (SAM input) .. ok
250s
250s 212: Count -x RG -r grp2 (SAM input) .. ok
250s
250s 213: Filter -x RG -r grp2 (BAM input) .. ok
250s
250s 214: Count -x RG -r grp2 (BAM input) .. ok
250s
251s 215: Filter -x RG -r grp2 (CRAM input) .. ok
251s
251s 216: Count -x RG -r grp2 (CRAM input) .. ok
251s
251s 217: Filter -m 10 (SAM input) .. ok
251s
251s 218: Count -m 10 (SAM input) .. ok
251s
251s 219: Filter -m 10 (BAM input) .. ok
251s
251s 220: Count -m 10 (BAM input) .. ok
251s
251s 221: Filter -m 10 (CRAM input) .. ok
251s
252s 222: Count -m 10 (CRAM input) .. ok
252s
252s 223: Filter -m 11 (SAM input) .. ok
252s
252s 224: Count -m 11 (SAM input) .. ok
252s
252s 225: Filter -m 11 (BAM input) .. ok
252s
252s 226: Count -m 11 (BAM input) .. ok
252s
252s 227: Filter -m 11 (CRAM input) .. ok
252s
252s 228: Count -m 11 (CRAM input) .. ok
252s
252s 229: Filter -m 15 (SAM input) .. ok
252s
252s 230: Count -m 15 (SAM input) .. ok
252s
252s 231: Filter -m 15 (BAM input) .. ok
252s
252s 232: Count -m 15 (BAM input) .. ok
252s
253s 233: Filter -m 15 (CRAM input) .. ok
253s
253s 234: Count -m 15 (CRAM input) .. ok
253s
253s 235: Filter -m 16 (SAM input) .. ok
253s
253s 236: Count -m 16 (SAM input) .. ok
253s
253s 237: Filter -m 16 (BAM input) .. ok
253s
253s 238: Count -m 16 (BAM input) .. ok
253s
253s 239: Filter -m 16 (CRAM input) .. ok
253s
254s 240: Count -m 16 (CRAM input) .. ok
254s
254s 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok
254s
254s 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok
254s
254s 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok
254s
254s 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok
254s
254s 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
254s
256s 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
256s
256s 247: Filter -e [BC] (SAM input) .. ok
256s
256s 248: Count -e [BC] (SAM input) .. ok
256s
256s 249: Filter -e [BC] (BAM input) .. ok
256s
256s 250: Count -e [BC] (BAM input) .. ok
256s
256s 251: Filter -e [BC] (CRAM input) .. ok
256s
256s 252: Count -e [BC] (CRAM input) .. ok
256s
256s 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
256s
256s 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
256s
256s 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
256s
256s 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
256s
257s 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
257s
258s 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
258s
258s 259: Filter -e mapq >= 50 (SAM input) .. ok
258s
258s 260: Count -e mapq >= 50 (SAM input) .. ok
258s
258s 261: Filter -e mapq >= 50 (BAM input) .. ok
258s
258s 262: Count -e mapq >= 50 (BAM input) .. ok
258s
259s 263: Filter -e mapq >= 50 (CRAM input) .. ok
259s
259s 264: Count -e mapq >= 50 (CRAM input) .. ok
259s
259s 265: Filter -e mapq >= 99 (SAM input) .. ok
259s
259s 266: Count -e mapq >= 99 (SAM input) .. ok
259s
259s 267: Filter -e mapq >= 99 (BAM input) .. ok
259s
259s 268: Count -e mapq >= 99 (BAM input) .. ok
259s
260s 269: Filter -e mapq >= 99 (CRAM input) .. ok
260s
260s 270: Count -e mapq >= 99 (CRAM input) .. ok
260s
260s 271: Filter -e mapq >= 100 (SAM input) .. ok
260s
260s 272: Count -e mapq >= 100 (SAM input) .. ok
260s
260s 273: Filter -e mapq >= 100 (BAM input) .. ok
260s
260s 274: Count -e mapq >= 100 (BAM input) .. ok
260s
260s 275: Filter -e mapq >= 100 (CRAM input) .. ok
260s
261s 276: Count -e mapq >= 100 (CRAM input) .. ok
261s
261s 277: 1bp reads file SAM -> BAM -> SAM .. ok
261s
261s 278: 1bp reads file SAM -> CRAM -> SAM .. ok
261s
262s 278: Region Z (BAM input) .. ok
262s
262s 279: Count Z (BAM input) .. ok
262s
262s 280: Region Z (CRAM input) .. ok
262s
262s 281: Count Z (CRAM input) .. ok
262s
262s 282: Region Z:30 (BAM input) .. ok
262s
262s 283: Count Z:30 (BAM input) .. ok
262s
262s 284: Region Z:30 (CRAM input) .. ok
262s
262s 285: Count Z:30 (CRAM input) .. ok
262s
262s 286: Region Z:20-40 (BAM input) .. ok
262s
262s 287: Count Z:20-40 (BAM input) .. ok
262s
263s 288: Region Z:20-40 (CRAM input) .. ok
263s
263s 289: Count Z:20-40 (CRAM input) .. ok
263s
263s 290: Region ref1 (BAM input) .. ok
263s
263s 291: Count ref1 (BAM input) .. ok
263s
263s 292: Region ref1 (CRAM input) .. ok
263s
263s 293: Count ref1 (CRAM input) .. ok
263s
263s 294: Region ref1:15 (BAM input) .. ok
263s
263s 295: Count ref1:15 (BAM input) .. ok
263s
264s 296: Region ref1:15 (CRAM input) .. ok
264s
264s 297: Count ref1:15 (CRAM input) .. ok
264s
264s 298: Region ref1:15-45 (BAM input) .. ok
264s
264s 299: Count ref1:15-45 (BAM input) .. ok
264s
264s 300: Region ref1:15-45 (CRAM input) .. ok
264s
264s 301: Count ref1:15-45 (CRAM input) .. ok
264s
264s 302: Region ref1:15-45 ref2 (BAM input) .. ok
264s
264s 303: Count ref1:15-45 ref2 (BAM input) .. ok
264s
265s 304: Region ref1:15-45 ref2 (CRAM input) .. ok
265s
265s 305: Count ref1:15-45 ref2 (CRAM input) .. ok
265s
265s 306: Region ref1:15-45 ref2:16 (BAM input) .. ok
265s
265s 307: Count ref1:15-45 ref2:16 (BAM input) .. ok
265s
265s 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok
265s
265s 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok
265s
265s 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
265s
265s 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
265s
266s 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
266s
266s 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
266s
266s 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
266s
266s 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
266s
266s 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
266s
266s 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
266s
266s 318: Region -f 128 ref1 (BAM input) .. ok
266s
266s 319: Count -f 128 ref1 (BAM input) .. ok
266s
266s 320: Region -f 128 ref1 (CRAM input) .. ok
266s
266s 321: Count -f 128 ref1 (CRAM input) .. ok
266s
266s 322: Region -q 50 ref1:15-45 (BAM input) .. ok
266s
266s 323: Count -q 50 ref1:15-45 (BAM input) .. ok
266s
267s 324: Region -q 50 ref1:15-45 (CRAM input) .. ok
267s
267s 325: Count -q 50 ref1:15-45 (CRAM input) .. ok
267s
267s 326: Region -r grp2 ref1:15-45 (BAM input) .. ok
267s
267s 327: Count -r grp2 ref1:15-45 (BAM input) .. ok
267s
267s 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok
267s
267s 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok
267s
267s 330: Region * (BAM input) .. ok
267s
267s 331: Count * (BAM input) .. ok
267s
267s 332: Region * (CRAM input) .. ok
267s
267s 333: Count * (CRAM input) .. ok
267s
267s 334: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok
267s
267s 335: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed (BAM input).. ok
267s
268s 336: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok
268s
268s 337: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed (CRAM input).. ok
268s
268s 338: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok
268s
268s 339: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.02.bed (BAM input).. ok
268s
268s 340: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok
268s
268s 341: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.02.bed (CRAM input).. ok
268s
268s 342: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok
268s
268s 343: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed (BAM input).. ok
268s
269s 344: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok
269s
269s 345: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed (CRAM input).. ok
269s
269s 346: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok
269s
269s 347: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.02.bed (BAM input).. ok
269s
269s 348: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok
269s
269s 349: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.02.bed (CRAM input).. ok
269s
269s 350: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok
269s
269s 351: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.03.bed (BAM input).. ok
269s
270s 352: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok
270s
270s 353: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.03.bed (CRAM input).. ok
270s
270s 354: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok
270s
270s 355: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z (BAM input).. ok
270s
270s 356: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok
270s
270s 357: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z (CRAM input).. ok
270s
270s 358: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok
270s
270s 359: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (BAM input).. ok
270s
271s 360: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
271s
271s 361: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
271s
271s 362: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
271s
271s 363: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
271s
271s 364: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
271s
271s 365: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
271s
271s 366: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
271s
271s 367: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
271s
272s 368: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
272s
272s 369: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
272s
272s 370: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
272s
272s 371: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
272s
272s 372: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
272s
272s 373: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
272s
272s 374: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok
272s
272s 375: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (BAM input).. ok
272s
272s 376: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok
272s
272s 377: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref2 (CRAM input).. ok
272s
272s 378: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
272s
272s 379: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
272s
273s 380: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
273s
273s 381: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
273s
273s 382: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
273s
273s 383: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
273s
273s 384: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
273s
273s 385: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
273s
273s 386: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok
273s
273s 387: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (BAM input).. ok
273s
274s 388: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
274s
274s 389: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
274s
274s 390: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok
274s
274s 391: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (BAM input).. ok
274s
274s 392: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
274s
274s 393: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
274s
274s 394: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
274s
274s 395: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
274s
275s 396: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
275s
275s 397: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
275s
275s 398: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
275s
275s 399: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
275s
275s 400: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
275s
275s 401: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
275s
275s 402: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
275s
275s 403: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
275s
276s 404: Region -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
276s
276s 405: Count -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
276s
276s 406: -L with nested regions .. ok
276s
276s 407: Make BAM with no M5/UR tags .. ok
276s
276s 408: Add @SQ with -t (SAM -> SAM) .. ok
276s
276s 409: Add @SQ with -T (SAM -> SAM) .. ok
276s
276s 410: Add @SQ with -t (BAM -> SAM) .. ok
276s
276s 411: Add @SQ with -T (BAM -> SAM) .. ok
276s
276s 412: Add @SQ with -t (SAM -> BAM) .. ok
276s
276s 413: Add @SQ with -T (SAM -> BAM) .. ok
276s
276s 414: Add @SQ with -t (BAM -> BAM) .. ok
276s
276s 415: Add @SQ with -T (BAM -> BAM) .. ok
276s
276s 416: Add @SQ with -t (SAM -> CRAM) .. ok
276s
277s 417: Add @SQ with -T (SAM -> CRAM) .. ok
277s
277s 418: Add @SQ with -t (BAM -> CRAM) .. ok
277s
278s 419: Add @SQ with -T (BAM -> CRAM) .. ok
278s
278s 420: Make CRAM with no UR field .. ok
278s
278s 421: Decoding CRAM with no UR field via -T .. ok
278s
278s 422: CIGAR B-operator removal .. ok
278s
278s 423: Big SAM -> BAM .. ok
278s
279s 424: Big SAM -> BAM (2 threads) .. ok
279s
280s 425: Big SAM -> BAM (4 threads) .. ok
280s
282s 426: Big SAM -> CRAM .. ok
282s
284s 427: Big SAM -> CRAM (2 threads) .. ok
284s
286s 428: Big SAM -> CRAM (4 threads) .. ok
286s
288s 429: Subsample 0.2 (SAM input) ............ ok
288s
290s 430: Subsample 0.5 (SAM input) ............ ok
290s
294s 431: Subsample 0.8 (SAM input) ............ ok
294s
295s 432: Subsample 0.2 (BAM input) ............ ok
295s
297s 433: Subsample 0.5 (BAM input) ............ ok
297s
300s 434: Subsample 0.8 (BAM input) ............ ok
300s
305s 435: Subsample 0.2 (CRAM input) ............ ok
305s
311s 436: Subsample 0.5 (CRAM input) ............ ok
311s
318s 437: Subsample 0.8 (CRAM input) ............ ok
318s
318s 438: SAM add PG .. ok
318s
318s 439: Unset dup flag, remove dt and do tags .. ok
318s
318s 440: Unmap dup flagged reads. .. ok
318s
318s 441: Unmap dup flagged reads. .. ok
318s
318s 442: fetch pairs .. ok
318s
318s 443: fetch pairs .. ok
318s
318s 444: fetch pairs .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -h 0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -h 1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -h 5 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -h 29 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -h 30 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -n 0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -n 1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -n 5 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_head:
318s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools head -h 5 -n 5 < /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.sam
318s .. ok
318s
318s test_cat:
319s Generating test data file .................. done
319s Generate BAM file #1 .. ok
319s
319s Generate BAM region file #1 .. ok
319s
319s Generate CRAM file #1 .. ok
319s
319s Generating test data file .................. done
319s Generate BAM file #2 .. ok
319s
319s Generate BAM region file #2 .. ok
319s
320s Generate CRAM file #2 .. ok
320s
320s Generating test data file .................. done
320s Generate BAM file #3 .. ok
320s
320s Generate BAM region file #3 .. ok
320s
320s Generate CRAM file #3 .. ok
320s
320s Generating test data file .................. done
320s Generate BAM file #4 .. ok
320s
320s Generate BAM region file #4 .. ok
320s
321s Generate CRAM file #4 .. ok
321s
321s 1: cat BAM files .. ok
321s
321s 2: cat recompressed BAM files .. ok
321s
321s 3: cat CRAM files .. ok
321s
323s 4: cat CRAM subregion files .. ok
323s
323s 5: cat BAM files to stdout .. ok
323s
323s 6: cat recompressed BAM files to stdout .. ok
323s
324s 7: cat CRAM files to stdout .. ok
324s
326s 8: cat CRAM subregion files to stdout .. ok
326s
326s 9: cat CRAM part 1/2 .. ok
326s
326s 9: cat CRAM part 2/2 .. ok
326s
326s 9: cat CRAM parts 1/2 + 2/2 .. ok
326s
327s 10: cat BAM files with new header .. ok
327s
327s 11: cat recompressed BAM files with new header .. ok
327s
327s 12: cat CRAM files with new header .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/0.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/0.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -T RG,BC,QT,MD,ia -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq
327s .. ok
327s
327s test_import:
327s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid'
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/import/2.interleaved.fq -T ""
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/import/3.interleaved.fq -i
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T "*"
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T ""
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
328s .. ok
328s
328s test_import:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
328s .. ok
328s
328s test_bam2fq:
328s Generate BAM file .. ok
328s
328s Generate CRAM file .. ok
328s
328s 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
328s [M::bam2fq_mainloop] processed 36 reads
328s .. ok
328s
328s 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
328s [M::bam2fq_mainloop] processed 36 reads
328s .. ok
328s
328s 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
328s [M::bam2fq_mainloop] processed 36 reads
328s .. ok
328s
328s 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
328s [M::bam2fq_mainloop] processed 36 reads
328s .. ok
328s
328s 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
328s [M::bam2fq_mainloop] processed 36 reads
328s .. ok
328s
328s 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
328s [M::bam2fq_mainloop] processed 36 reads
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.002.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.003.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.004.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.004.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.010.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -t -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -t -T MD,ia -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.004.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -i --index-format 'i*i*' -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.703.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fasta -N -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -s /tmp/mTCQSioAb_/bam2fq.discard.s.fq -0 /tmp/mTCQSioAb_/bam2fq.discard.0.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.013.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq --index-format 'i8n1i8' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.014.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -T '' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -t -T '*' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -T '*' -d MD:10 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -T '*' -d NM:0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -N -T '*' -d ia /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -d NM:13 -d NM:14 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
328s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
328s .. ok
328s
328s test_bam2fq:
329s Generate BAM file (2 threads) .. ok
329s
329s Generate CRAM file (2 threads) .. ok
329s
329s 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
329s [M::bam2fq_mainloop] processed 36 reads
329s .. ok
329s
329s 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
329s [M::bam2fq_mainloop] processed 36 reads
329s .. ok
329s
329s 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
329s [M::bam2fq_mainloop] processed 36 reads
329s .. ok
329s
329s 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
329s [M::bam2fq_mainloop] processed 36 reads
329s .. ok
329s
329s 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
329s [M::bam2fq_mainloop] processed 36 reads
329s .. ok
329s
329s 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
329s [M::bam2fq_mainloop] processed 36 reads
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.002.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.003.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.004.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.004.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.010.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bc_split.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -t -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T MD,ia -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.004.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i.fq -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -i --index-format 'i*i*' -s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/s.fq -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.005.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/1.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/2.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.703.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fq -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fasta -@ 2 -N -1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fa -2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/o.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -s /tmp/mTCQSioAb_/bam2fq.discard.s.fq -0 /tmp/mTCQSioAb_/bam2fq.discard.0.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.013.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i1.fq --i2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/i2.fq -0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/0.fq /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.014.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -T '' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
329s .. ok
329s
329s test_bam2fq:
329s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -t -T '*' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_bam2fq:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d MD:10 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_bam2fq:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d NM:0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_bam2fq:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -N -T '*' -d ia /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_bam2fq:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -d NM:13 -d NM:14 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_bam2fq:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_bam2fq:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/bam2fq.001.sam
330s .. ok
330s
330s test_depad:
330s Generate BAM file .. ok
330s
330s depad (SAM input) .. ok
330s
330s depad -s (SAM input) .. ok
330s
330s depad -u (SAM input) .. ok
330s
330s depad -1 (SAM input) .. ok
330s
330s depad (BAM input) .. ok
330s
330s depad -s (BAM input) .. ok
330s
330s depad -u (BAM input) .. ok
330s
330s depad -1 (BAM input) .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/1_map_cigar_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/4_X_cigar_full_seq.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/5_insert_cigar_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa -i 0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/5_insert_cigar.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/7_supp.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/7_supp_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/8_secondary.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/8_secondary_large.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/1_map_cigar.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -S RG -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/test.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/10_map_cigar.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -t /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -g 4 -t /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11.stats.targets /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.sam | tail -n+4
330s .. ok
330s
330s test_stats:
330s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -g 4 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_3reads.bed | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_overlaps.bam -t /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_overlaps.bam -p -t /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/12_2reads.bed | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13_barcodes_ok.sam | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4
331s
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory
331s .. expected failure
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4
331s
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory
331s .. expected failure
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4
331s
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/13.barcodes.fail.expected: No such file or directory
331s .. expected failure
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -I s1 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -I grp2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -I grp3 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -I Sample /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/11_target.bam | tail -n+4
331s .. ok
331s
331s test_stats:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools stats -r /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/mpileup/ce.fa /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/stat/15.big_del.sam | tail -n+4
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -O sam -b /tmp/sFp3MMiyYH - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -r -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -cp -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -o - -s 1 -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/mTCQSioAb_/merge.tag.1.bam /tmp/mTCQSioAb_/merge.tag.2.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/mTCQSioAb_/merge.tag.3.bam /tmp/mTCQSioAb_/merge.tag.4.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge --no-PG -O SAM - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge --no-PG -O SAM -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/merge.bed - /tmp/mTCQSioAb_/merge.bed.1.bam /tmp/mTCQSioAb_/merge.bed.2.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge --no-PG -r -O SAM - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam -b /tmp/eFUvHKhn_U - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -r -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -cp -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -O sam - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a_regex.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b_regex.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -o - -s 1 -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_c.sam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/mTCQSioAb_/merge.tag.1.bam /tmp/mTCQSioAb_/merge.tag.2.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/mTCQSioAb_/merge.tag.3.bam /tmp/mTCQSioAb_/merge.tag.4.bam
331s .. ok
331s
331s test_merge:
331s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam
332s .. ok
332s
332s test_merge:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/merge.bed - /tmp/mTCQSioAb_/merge.bed.1.bam /tmp/mTCQSioAb_/merge.bed.2.bam
332s .. ok
332s
332s test_merge:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 --no-PG -r -O SAM - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_no_pg_rg_co.sam
332s .. ok
332s
332s test_merge:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_template_coordinate.1.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/merge/test_template_coordinate.2.sam
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/mTCQSioAb_/sortout
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/mTCQSioAb_/sortout.bam
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/mTCQSioAb_/sorttmp
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -N -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -n -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -t RG -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -n -t RG -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -t AS -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -t FI -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort --template-coordinate -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -M -K10 -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -M -K10 -I /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -MH -K10 -I /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/mTCQSioAb_/sortout
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/mTCQSioAb_/sortout.bam
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam /tmp/mTCQSioAb_/sorttmp
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -N -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_b.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -n -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/sort_name_input_1.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -t RG -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -n -t RG -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -t AS -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -t FI -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 --template-coordinate -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/sort/template-coordinate.sort.sam -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -M -K10 -I /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o -
332s .. ok
332s
332s test_sort:
332s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/auto_indexed.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -@ 2 -MH -K10 -I /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.ref.fa -O SAM -o -
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate --output-fmt=sam -O /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate2.tmp
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate --output-fmt=sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate3.tmp
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate --output-fmt=sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/1_fast_collate.sam
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate --output-fmt=sam -f -r 4 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam
333s .. ok
333s
333s test_collate:
333s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -O /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam
335s .. ok
335s
335s test_collate:
335s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate1.tmp.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam
336s .. ok
336s
336s test_collate:
336s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -@ 2 -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate2.tmp.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate2.tmp
337s .. ok
337s
337s test_collate:
337s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_d.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/collate3.tmp
338s .. ok
338s
338s test_collate:
338s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/1_fast_collate.sam
339s .. ok
339s
339s test_collate:
339s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools collate -@ 2 --output-fmt=sam -f -r 4 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/fast_collate.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/collate/2_fast_collate_with_tmp.sam
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/1_coord_sort.sam -
340s
340s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
340s
340s .. expected failure
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/5_ct.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -cO sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/6_ct_replace.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/sanitize.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ok+.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ok-.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_draft.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_not_updated.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_MN_only.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ML_only.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_noseq.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_bounds.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/1_coord_sort.sam -
340s
340s ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
340s
340s .. expected failure
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/2_isize_overflow.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/3_reverse_read_pp_lt.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/4_reverse_read_pp_equal.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/5_ct.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -cO sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/6_ct_replace.sam -
340s .. ok
340s
340s test_fixmate:
340s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/7_two_read_mapped.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/8_isize_overflow_64bit.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/sanitize.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ok+.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ok-.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_draft.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_not_updated.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_not_updated_noML.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_not_updated_noMN.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_bad_MN.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_MN_only.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ML_only.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_ML_wrong_len.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_noseq.sam -
341s .. ok
341s
341s test_fixmate:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -@ 2 -M -z off -O sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/fixmate/mod_bounds.sam -
341s .. ok
341s
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools calmd -uAr /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.ref.fa
341s .. ok
341s
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools calmd -@ 2 -uAr /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.ref.fa
341s .. ok
341s
341s test_idxstat:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam
341s .. ok
341s
341s test_idxstat:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.cram
341s .. ok
341s
341s test_idxstat:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools idxstats /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.sam
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck -v /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/1.quickcheck.badeof.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/2.quickcheck.badheader.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/3.quickcheck.ok.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/4.quickcheck.ok.bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/5.quickcheck.scramble30.truncated.cram /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/6.quickcheck.cram21.ok.cram /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/7.quickcheck.cram30.ok.cram /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/8.quickcheck.cram21.truncated.cram /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/9.quickcheck.cram30.truncated.cram /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
341s .. ok
341s
341s test_quickcheck:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools quickcheck -uv /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
341s .. ok
341s
341s test_reheader:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
341s .. ok
341s
341s test_reheader:
341s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
342s .. ok
342s
342s test_reheader:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
342s .. ok
342s
342s test_reheader:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram && /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
342s .. ok
342s
342s test_reheader:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader --in-place /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reheader/hdr.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram && /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
342s .. ok
342s
342s test_reheader:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.bam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
342s .. ok
342s
342s test_reheader:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/view.001.tmp.v30.cram | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -m orphan_only /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -R '1#9' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m orphan_only /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/2_fixup_orphan.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -R '1#9' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/4_fixup_norg.sam
342s .. ok
342s
342s test_addrprg:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/addrprg/1_fixup.sam
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/1_name_sort.sam -
342s
342s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/2_bad_order.sam -
342s
342s ERR: samtools markdup: error, not in coordinate sorted order.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/3_missing_mc.sam -
342s
342s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.
342s
342s samtools markdup: error, unable to assign pair hash key.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/4_missing_ms.sam -
342s
342s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
342s
342s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/5_markdup.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -O sam -r --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/6_remove_dups.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/8_optical_dup.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/10_optical_chain.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/10_optical_chain.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/17_read_group.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam -
342s .. ok
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/1_name_sort.sam -
342s
342s ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/2_bad_order.sam -
342s
342s ERR: samtools markdup: error, not in coordinate sorted order.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/3_missing_mc.sam -
342s
342s ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.
342s
342s samtools markdup: error, unable to assign pair hash key.
342s
342s
342s .. expected failure
342s
342s test_markdup:
342s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/4_missing_ms.sam -
343s
343s ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
343s
343s samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
343s
343s
343s .. expected failure
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/5_markdup.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -O sam -r --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/6_remove_dups.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/7_mark_supp_dup.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/8_optical_dup.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/9_optical_dup_qcfail.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/10_optical_chain.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/10_optical_chain.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/11_optical_dup_regex.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/12_optical_chain_regex.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/13_optical_barcode_tag.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/14_optical_barcode_name.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/15_optical_barcode_rgx_name.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/17_read_group.sam -
343s .. ok
343s
343s test_markdup:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/markdup/18_primary_duplicate_count.sam -
343s .. ok
343s
343s test_bedcov:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools bedcov /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov.bam
343s .. ok
343s
343s test_bedcov:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools bedcov -j /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov.bam
343s .. ok
343s
343s test_bedcov:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools bedcov -g512 -G2048 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov.bam
343s .. ok
343s
343s test_bedcov:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools bedcov -c /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov_gG.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/bedcov/bedcov.bam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -d RG -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -d an -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split_d_nn.sam
343s .. ok
343s
343s test_split:
343s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split --output-fmt sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split_d_nn.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -p 5 -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%#.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d RG -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.unk.sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.%!.%. /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -d nn -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.unk.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split_d_nn.sam
344s .. ok
344s
344s test_split:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools split -@ 2 --output-fmt sam -f /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split.tmp.d_nn.0unk.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/split/split_d_nn.sam
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG /tmp/mTCQSioAb_/longref.sam.gz
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG /tmp/mTCQSioAb_/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view -h --no-PG -L /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/test.bed /tmp/mTCQSioAb_/longref.sam.gz
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/longref_name.sam
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools merge -O sam --no-PG - /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/longref.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/longref2.sam
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools depth /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/longref.sam
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools depth -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/large_pos/longref.sam
344s .. ok
344s
344s test_large_positions:
344s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/mTCQSioAb_/longref.sam.gz
345s .. ok
345s
345s test_large_positions:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools fixmate -O sam --no-PG - - |
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools sort -O sam --no-PG -m 10M
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --primer-counts /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/2_both_test_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/primer_counts.tsv -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/3_multi_ref_data.sam
345s .. ok
345s
345s test_ampliconclip:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test2.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/4_total_hc_data.sam
345s .. ok
345s
345s test_ampliconstats:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_hard_clipped.expected.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_soft_clipped.expected.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/1_soft_clipped_strand.expected.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line'
345s .. ok
345s
345s test_ampliconstats:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/multi_ref.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
345s .. ok
345s
345s test_ampliconstats:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools ampliconstats -@ 2 -c 0 /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconclip/ac_test.bed /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
345s .. ok
345s
345s test_reset:
345s cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view
345s .. ok
345s
345s test_reset:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag < /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view
345s .. ok
345s
345s test_reset:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools view
345s .. ok
345s
345s test_reset:
345s cat /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam | /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam
345s .. ok
345s
345s test_reset:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.bam
345s .. ok
345s
345s test_reset:
345s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/test_input_1_a.cram
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g'
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG sam_to_fixed_bam /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g'
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index --no-PG /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam; grep /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output.tmp.sam -e"@PG"
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag --reject-PG bwa_index /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset --dupflag /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s test_reset:
346s /tmp/autopkgtest.ggncwL/autopkgtest_tmp/samtools reset /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/seq.sam -o /tmp/autopkgtest.ggncwL/autopkgtest_tmp/test/reset/output
346s .. ok
346s
346s
346s Number of tests:
346s total .. 951
346s passed .. 920
346s failed .. 0
346s expected failure .. 31
346s unexpected pass .. 0
346s
346s autopkgtest [17:24:22]: test run-unit-test: -----------------------]
350s autopkgtest [17:24:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
350s run-unit-test PASS
354s autopkgtest [17:24:30]: @@@@@@@@@@@@@@@@@@@@ summary
354s run-unit-test PASS