Michael R. Crusoe pushed to branch master at Debian Med / bwa-mem2
Commits: 2beaa4ed by Michael R. Crusoe at 2020-07-23T10:00:52+02:00 Add autopkgtests. - - - - - 7f448363 by Michael R. Crusoe at 2020-07-23T10:14:19+02:00 forward patches upstream - - - - - 11 changed files: - + debian/bwa-mem2.examples - debian/changelog - + debian/examples/read1.fq - + debian/examples/read2.fq - + debian/examples/reads.fq - + debian/examples/ref.fa - debian/patches/hardening - debian/patches/simde - debian/patches/spelling - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/bwa-mem2.examples ===================================== @@ -0,0 +1 @@ +debian/examples/* ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +bwa-mem2 (2.0-2) UNRELEASED; urgency=medium + + * Add autopkgtests. + + -- Michael R. Crusoe <[email protected]> Thu, 23 Jul 2020 09:44:17 +0200 + bwa-mem2 (2.0-1) unstable; urgency=medium * Initial release. (Closes: #950607) ===================================== debian/examples/read1.fq ===================================== @@ -0,0 +1,4 @@ +@HWUSI +GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC ++HWUSI +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh ===================================== debian/examples/read2.fq ===================================== @@ -0,0 +1,4 @@ +@HWUSI +CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG ++HWUSI +acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff ===================================== debian/examples/reads.fq ===================================== @@ -0,0 +1,16 @@ +@HWUSI +CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG ++HWUSI +acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff +@HWUSI +CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC ++HWUSI +hhhcfhhhhhhhhhhhhghhhhhhffhhhhhhhhhhhhhg +@HWUSI +AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG ++HWUSI +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhh +@HWUSI +GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC ++HWUSI +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh ===================================== debian/examples/ref.fa ===================================== @@ -0,0 +1,8 @@ +>HWUSI +CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG +>HWUSI +CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC +>HWUSI +AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG +>HWUSI +GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC ===================================== debian/patches/hardening ===================================== @@ -1,5 +1,6 @@ Author: Michael R. Crusoe <[email protected]> Description: Enable proper flag appending so that Debian can harden the build. +Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/69 --- bwa-mem2.orig/Makefile +++ bwa-mem2/Makefile @@ -37,7 +37,8 @@ ===================================== debian/patches/simde ===================================== @@ -1,5 +1,6 @@ From: Michael R. Crusoe <[email protected]> Subject: Enable building on non-x86 +Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/84 --- bwa-mem2.orig/src/FMI_search.h +++ bwa-mem2/src/FMI_search.h ===================================== debian/patches/spelling ===================================== @@ -1,5 +1,6 @@ From: Michael R. Crusoe <[email protected]> Subject: fix a typo +Forwarded: https://github.com/bwa-mem2/bwa-mem2/pull/83 --- bwa-mem2.orig/src/profiling.cpp +++ bwa-mem2/src/profiling.cpp @@ -57,7 +57,7 @@ ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,18 @@ +#!/bin/bash +set -e + +pkg="bwa-mem2" + +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi + +cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP + +bwa-mem2 index ref.fa +bwa-mem2 mem ref.fa reads.fq > aln-se.sam +bwa-mem2 mem ref.fa read1.fq read2.fq > aln-pe.sam + +echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426 -- View it on GitLab: https://salsa.debian.org/med-team/bwa-mem2/-/compare/18d063f78d51b58c00b69aa2cc5ca8d94abc3abc...7f44836367952bad93cebe969a6f27f9b706c426 You're receiving this email because of your account on salsa.debian.org.
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