Nilesh Patra pushed to branch master at Debian Med / samtools-legacy
Commits: a0953324 by Nilesh Patra at 2021-07-24T22:44:10+05:30 Add Depends on zlib1g-dev - - - - - 1678ceca by Nilesh Patra at 2021-07-24T22:44:28+05:30 Add autopkgtests - - - - - c8c7c707 by Nilesh Patra at 2021-07-24T22:47:28+05:30 Declare compliance with policy 4.5.1 - - - - - baa30d41 by Nilesh Patra at 2021-07-24T22:47:28+05:30 Interim changelog entry - - - - - 4 changed files: - debian/changelog - debian/control - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +samtools-legacy (0.1.19+dfsg-2) UNRELEASED; urgency=medium + + * Team Upload. + * Add Depends on zlib1g-dev + * Add autopkgtests + * Declare compliance with policy 4.5.1 + + -- Nilesh Patra <[email protected]> Sat, 24 Jul 2021 22:47:09 +0530 + samtools-legacy (0.1.19+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper-compat (= 13), libncurses5-dev, zlib1g-dev -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/samtools-legacy Vcs-Git: https://salsa.debian.org/med-team/samtools-legacy.git Homepage: https://www.htslib.org/ @@ -16,7 +16,8 @@ Package: libbam-dev Architecture: any Section: libdevel Depends: ${shlibs:Depends}, - ${misc:Depends} + ${misc:Depends}, + zlib1g-dev Description: manipulates nucleotide sequence alignments in BAM or SAM format The BAM library provides I/O and various operations on manipulating nucleotide sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, build-essential, samtools +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,34 @@ +#!/bin/bash +set -e + +pkg=cppnumericalsolvers +CUR_DIR=`pwd` + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cd "${AUTOPKGTEST_TMP}" +cp ${CUR_DIR}/examples/* . + +samtools view -S -b toy.sam > toy.bam + +echo "Test 1 -- calDepth" +gcc calDepth.c -o calDepth -I/usr/include/samtools -lbam -lm -lz -lpthread +./calDepth toy.bam +echo "=============== PASS ================" + +echo "Test 2 -- chk_indel" +gcc chk_indel.c -o chk_indel -I/usr/include/samtools -lbam -lm -lz -lpthread +./chk_indel toy.bam +echo "=============== PASS ================" + + +echo "Test 3 -- bam2bed" +gcc bam2bed.c -o bam2bed -I/usr/include/samtools -lbam -lm -lz -lpthread +./bam2bed toy.bam +echo "=============== PASS ================" + +rm -f toy.bam View it on GitLab: https://salsa.debian.org/med-team/samtools-legacy/-/compare/368be378d9ba419c664a00c8b60b893eda236262...baa30d41a44112f8d171783aca34c5f5cdfdb687 -- View it on GitLab: https://salsa.debian.org/med-team/samtools-legacy/-/compare/368be378d9ba419c664a00c8b60b893eda236262...baa30d41a44112f8d171783aca34c5f5cdfdb687 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
