Nilesh Patra pushed to branch master at Debian Med / wtdbg2
Commits: 6a3f4407 by Nilesh Patra at 2020-08-09T20:51:54+05:30 Simplify autopkgtest - - - - - 7f3984e6 by Nilesh Patra at 2020-08-09T20:55:22+05:30 Update changelog - - - - - 2 changed files: - debian/changelog - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +wtdbg2 (2.5-4) UNRELEASED; urgency=medium + + * Team Upload. + * Add autopkgtests + * Save up space by not extracting the binary + * New binary: wtdbg2-examples + * Minor fixes on manpages + * Fix spellings + + -- Nilesh Patra <[email protected]> Sun, 09 Aug 2020 20:28:18 +0530 + wtdbg2 (2.5-3) unstable; urgency=medium * Team upload. ===================================== debian/tests/run-unit-test ===================================== @@ -15,14 +15,6 @@ gunzip -r * tar -xvf *.tar cd selfSampleData -# Checks whether file checksum is same as expected -function check_same() -{ - # $1 : file name - # $2 : checksum value - [ "$(cat $1 | md5sum | awk '{print $1}')" == $2 ] || exit 1 -} - echo "Begin Execution" wtdbg2 -t 16 -x rs -g 4.6m -o dbg pacbio_filtered.fastq @@ -32,12 +24,12 @@ wtdbg2 -x rs -g 4.6m -i pacbio_filtered.fastq -t 16 -fo dbg # derive consensus wtpoa-cns -t 16 -i dbg.ctg.lay.gz -fo dbg.raw.fa -check_same dbg.raw.fa a2c479242d7c6ad6c8ffd979b821aa01 +[ -s dbg.raw.fa ] || exit 1 echo "PASS" # polish consensus, not necessary if you want to polish the assemblies using other tools minimap2 -t16 -ax map-pb -r2k dbg.raw.fa pacbio_filtered.fastq | samtools sort -@4 >dbg.bam samtools view -F0x900 dbg.bam | wtpoa-cns -t 16 -d dbg.raw.fa -i - -fo dbg.cns.fa -check_same dbg.cns.fa 62a41e5cb7a5e702523237f4ab65c376 +[ -s dbg.cns.fa ] || exit 1 echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/wtdbg2/-/compare/e56ba7735427e54e99ee73d083a4ee8a78724aa2...7f3984e67ca50a450205c92719a6d5de3bc704b1 -- View it on GitLab: https://salsa.debian.org/med-team/wtdbg2/-/compare/e56ba7735427e54e99ee73d083a4ee8a78724aa2...7f3984e67ca50a450205c92719a6d5de3bc704b1 You're receiving this email because of your account on salsa.debian.org.
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