[med-svn] [bwa] 01/01: Autopkgtests and example directory added

[Canberk Koç]

This is an automated email from the git hooks/post-receive script.

cbk-guest pushed a commit to branch master
in repository bwa.

commit 81356eb05a4ccfaac9f5eb866da3d8f8abe428de
Author: cbk-guest <cbk-guests at scm.alioth.debian.org>
Date:   Sat Jun 25 23:37:25 2016 +0300

    Autopkgtests and example directory added
---
 debian/bwa.examples        |  1 +
 debian/changelog           | 10 ++++++++--
 debian/examples/read1.fq   |  4 ++++
 debian/examples/read2.fq   |  4 ++++
 debian/examples/reads.fq   | 16 ++++++++++++++++
 debian/examples/ref.fa     |  8 ++++++++
 debian/tests/control       |  3 +++
 debian/tests/run-unit-test | 23 +++++++++++++++++++++++
 8 files changed, 67 insertions(+), 2 deletions(-)

diff --git a/debian/bwa.examples b/debian/bwa.examples
new file mode 100644
index 0000000..55b78ae
--- /dev/null
+++ b/debian/bwa.examples
@@ -0,0 +1 @@
+debian/examples/*
diff --git a/debian/changelog b/debian/changelog
index 769b6d8..9d67e71 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,16 @@
 bwa (0.7.15-1) unstable; urgency=medium
-
+  * team upload
+  
+  [ Andreas Tille ]
   * New upstream version
   * cme fix dpkg-control
   * better hardening
+  
+  [ Canberk Koç ]
+  * Added testsuite
+  * debian/examples directory added
 
- -- Andreas Tille <tille at debian.org>  Fri, 03 Jun 2016 17:53:03 +0200
+ -- Canberk Koç <canberkkoc at gmail.com>  Sat, 25 Jun 2016 23:36:31 +0300
 
 bwa (0.7.13-1) unstable; urgency=medium
 
diff --git a/debian/examples/read1.fq b/debian/examples/read1.fq
new file mode 100644
index 0000000..2292db9
--- /dev/null
+++ b/debian/examples/read1.fq
@@ -0,0 +1,4 @@
+ at HWUSI
+GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC
++HWUSI
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhhh
diff --git a/debian/examples/read2.fq b/debian/examples/read2.fq
new file mode 100644
index 0000000..0d0aa2f
--- /dev/null
+++ b/debian/examples/read2.fq
@@ -0,0 +1,4 @@
+ at HWUSI
+CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG
++HWUSI
+acdd^aa_Z^d^ddc`^_Q_aaa`_ddc\dfdffff\fff
diff --git a/debian/examples/reads.fq b/debian/examples/reads.fq
new file mode 100644
index 0000000..ef4abd4
--- /dev/null
+++ b/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
diff --git a/debian/examples/ref.fa b/debian/examples/ref.fa
new file mode 100644
index 0000000..0eb11c7
--- /dev/null
+++ b/debian/examples/ref.fa
@@ -0,0 +1,8 @@
+>HWUSI
+CGTAGCTGTGTGTACAAGGCCCGGGAACGTATTCACCGTG
+>HWUSI
+CGTAAATGGACAGCATGACCCGACATCCCACACTCGCCGC
+>HWUSI
+AGGGGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG
+>HWUSI
+GTCAGTGAAATCCTGTCTGAACATGGGGGGACCACCCTCC
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..94fa4b5
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,23 @@
+#!/bin/bash
+set -e
+
+pkg="bwa"
+
+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 index ref.fa
+bwa mem ref.fa reads.fq > aln-se.sam 
+bwa mem ref.fa read1.fq read2.fq > aln-pe.sam 
+bwa aln ref.fa read1.fq > aln_sa.sai
+bwa samse ref.fa aln_sa.sai read1.fq > aln-se.sam
+bwa aln ref.fa read2.fq > aln_sa2.sai
+bwa sampe ref.fa aln_sa.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
+bwa bwasw ref.fa reads.fq > aln.sam
+
+echo "PASS"

-- 
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