Pranav Ballaney pushed to branch master at Debian Med / biobambam2
Commits: 39c199bd by Pranav Ballaney at 2020-05-27T16:52:08+05:30 Add autopkgtest data - - - - - 0074ebd4 by Pranav Ballaney at 2020-05-27T16:52:20+05:30 Add autopkgtests - - - - - f528447e by Pranav Ballaney at 2020-05-27T16:52:45+05:30 Install manpages and docs - - - - - 10 changed files: - + debian/README.test - + debian/docs - + debian/examples - + debian/manpages - + debian/source/include-binaries - + debian/tests/control - + debian/tests/data/README.test-data - + debian/tests/data/SRR11728627.bam - + debian/tests/data/SRR11728641.bam - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/docs ===================================== @@ -0,0 +1,5 @@ +README +README.md +debian/README.test +debian/tests/run-unit-test +debian/tests/data/README.test-data ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/data/* \ No newline at end of file ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +src/programs/*.1 \ No newline at end of file ===================================== debian/source/include-binaries ===================================== @@ -0,0 +1,2 @@ +debian/tests/data/SRR11728627.bam +debian/tests/data/SRR11728641.bam \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/data/README.test-data ===================================== @@ -0,0 +1,12 @@ +The files used for testing were obtained by downloading the following: +* NC_045512.2.fasta from https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta +* SRR11728627.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728627 +* SRR11728641.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728641 + +And applying the following operations: + +bowtie2-build NC_045512.2.fasta sars-cov-2 +bowtie2 -x sars-cov-2 SRR11728627.fq -S SRR11728627.sam +bowtie2 -x sars-cov-2 SRR11728641.fq -S SRR11728641.sam +samtools view -b SRR11728627.sam > SRR11728627.bam +samtools view -b SRR11728641.sam > SRR11728641.bam \ No newline at end of file ===================================== debian/tests/data/SRR11728627.bam ===================================== Binary files /dev/null and b/debian/tests/data/SRR11728627.bam differ ===================================== debian/tests/data/SRR11728641.bam ===================================== Binary files /dev/null and b/debian/tests/data/SRR11728641.bam differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,58 @@ +#!/bin/bash +set -e + +pkg=biobambam2 + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +echo -e "\e[93m\e[1mTest 1\e[0m" +bamsormadup < SRR11728627.bam > SRR11728627.sorted.bam +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 2\e[0m" +bamcollate2 index=1 collate=3 indexfilename=SRR11728627.idx < SRR11728627.bam > SRR11728627.collated.bam +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 3\e[0m" +bammarkduplicates2 I=SRR11728641.bam O=SRR11728641.uniq.bam D=SRR11728641.dups.bam rmdup=1 +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 4\e[0m" +bammarkduplicates2 I=SRR11728641.bam O=SRR11728641.dupmarked.bam md5=1 md5filename=SRR11728641.dupmarked.bam.md5 +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 5\e[0m" +bammaskflags maskneg=16 < SRR11728627.bam > SRR11728627.masked.bam +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 6\e[0m" +bamrecompress level=3 < SRR11728627.sam > SRR11728627.lvl3.bam +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 7\e[0m" +bamsort SO=coordinate < SRR11728641.bam > SRR11728641.sorted.bam +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 8\e[0m" +bamtofastq collate=1 < SRR11728627.bam > SRR11728627.fastq +echo -e "\e[92m\e[1mPassed\e[0m" +echo + View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/565373b5d1ead2f045943e270d479ad8366dd310...f528447efb7ccca633f69109c289c257e6edc5c2 -- View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/565373b5d1ead2f045943e270d479ad8366dd310...f528447efb7ccca633f69109c289c257e6edc5c2 You're receiving this email because of your account on salsa.debian.org.
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