[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.2-45-g633df70

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 553bf45b2bc8a456bc89f7002cfb461a4d0e17f5
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Nov 19 12:17:45 2012 +0100

    a bit improved test

diff --git a/debian/tests/indexing_ref_genome b/debian/tests/indexing_ref_genome
index 3d7de12..8a69c36 100755
--- a/debian/tests/indexing_ref_genome
+++ b/debian/tests/indexing_ref_genome
@@ -5,5 +5,11 @@ pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
 examplesdir=/usr/share/doc/$pkg/examples
 WORKDIR=$(mktemp -d)
 cd $WORKDIR
-zcat $examplesdir/reference/lambda_virus.fa.gz >lambda_virus.fa
+for file in reference/lambda_virus.fa.gz reads/reads_1.fq.gz 
+do
+	extracted=`echo $file | awk -F/ '{print $NF}'`
+        zcat $examplesdir/$file >${extracted%.gz}
+done
+
 bowtie2-build lambda_virus.fa lambda_virus >/dev/null 2>&1 
+bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam >/dev/null 2>&1

-- 
ultrafast memory-efficient short read aligner