[med-svn] [Git][med-team/bwa-mem2][master] 2 commits: Add autopkgtests.

[Michael R. Crusoe]

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 <crusoe at debian.org>  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 @@
+ at HWUSI
+GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC
++HWUSI
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh


=====================================
debian/examples/read2.fq
=====================================
@@ -0,0 +1,4 @@
+ at HWUSI
+CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG
++HWUSI
+acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff


=====================================
debian/examples/reads.fq
=====================================
@@ -0,0 +1,16 @@
+ at HWUSI
+CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG
++HWUSI
+acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff
+ at HWUSI
+CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC
++HWUSI
+hhhcfhhhhhhhhhhhhghhhhhhffhhhhhhhhhhhhhg
+ at HWUSI
+AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG
++HWUSI
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhh
+ at 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 <crusoe at debian.org>
 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 <crusoe at debian.org>
 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 <crusoe at debian.org>
 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
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