Nilesh Patra pushed to branch master at Debian Med / tiddit
Commits: eafa7abb by Nilesh Patra at 2020-10-06T22:41:10+05:30 Simplify autopkgtest (Closes: #964101) - - - - - a14b7944 by Nilesh Patra at 2020-10-06T22:44:59+05:30 Update changelog - - - - - 4 changed files: - debian/changelog - debian/tests/README.md - − debian/tests/data/ref.fa - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +tiddit (2.12.0+dfsg-3) UNRELEASED; urgency=medium + + * Team Upload. + * Simplify autopkgtest (Closes: #964101) + + -- Nilesh Patra <[email protected]> Tue, 06 Oct 2020 22:41:27 +0530 + tiddit (2.12.0+dfsg-2) unstable; urgency=medium * Team Upload. ===================================== debian/tests/README.md ===================================== @@ -1,18 +1,6 @@ Data for tiddit ===================== -The data is from NA12878 (tumor) and NA12892 (normal) and represents a tiny chunk of chromsome 21. It was created from 1000 Genomes Project (http://www.1000genomes.org) data available in the following locations: -* NA12892 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12892/high_coverage_alignment/NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam -* NA12878 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam -* Build 37 reference - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz + The test data for tiddit has been referenced from here: https://github.com/genome/somatic-snv-test-data which has further steps for creating the data + All work is from public datasets and have been made with tools in the open domain. -Should you wish to recreate the files in this repository, they were processed as follows below. - - samtools view -hb NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam 21:10400000-10500000 > normal.bam - samtools view -hb NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam 21:10400000-10500000 > tumor.bam - gunzip human_g1k_v37.fasta.gz - samtools faidx human_g1k_v37.fasta 21:1-10505000 > ref.fa - samtools view -h -o normal.sam normal.bam - samtools view -h -o tumor.sam tumor.bam - -Note that ref.fa was then further edited to change the chromosome name back to 21 as faidx includes the requested region in the name. ===================================== debian/tests/data/ref.fa deleted ===================================== The diff for this file was not included because it is too large. ===================================== debian/tests/run-unit-test ===================================== @@ -17,10 +17,24 @@ cat normal.sam | samtools view -Sb - > normal.bam cat tumor.sam | samtools view -Sb - > tumor.bam echo 'Test 1' -TIDDIT.py --sv --p_ratio 0.10 --bam tumor.bam -o test1 --ref ref.fa +TIDDIT --cov -b normal.bam -o test1 +TIDDIT --cov -w -b normal.bam -o test1 +for f in test1.* +do + [ -s $f ] || exit 1 + cat $f | tail -20 +done +rm -f ./test1* echo 'PASS' echo 'Test 2' -TIDDIT.py --sv --bam normal.bam -o test2 --ref ref.fa +TIDDIT --cov -b normal.bam -o test2 +TIDDIT --cov -w -b tumor.bam -o test2 +for f in test2.* +do + [ -s $f ] || exit 1 + cat $f | tail -20 +done +rm -f ./test2* echo 'PASS' View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b -- View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
