[med-svn] [subread] 05/05: d/tests/control d/tests/subread-align: new test

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit c11dda0e3cd5edb774fdf9d33a329fe884645ddf
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Mar 11 15:52:11 2015 +0100

    d/tests/control
    d/tests/subread-align: new test
---
 debian/tests/control       |  2 ++
 debian/tests/subread-align | 13 +++++++++++++
 2 files changed, 15 insertions(+)

diff --git a/debian/tests/control b/debian/tests/control
index 8d2fc14..415f1e5 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -3,3 +3,5 @@ Tests: exactSNP
 Tests: fc-minimal
 
 Tests: subjunc
+
+Tests: subread-align
diff --git a/debian/tests/subread-align b/debian/tests/subread-align
new file mode 100755
index 0000000..3f1a904
--- /dev/null
+++ b/debian/tests/subread-align
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+set -e
+workdir=test/subread-align
+cd $workdir
+tmpdir=$(mktemp -d)
+subread-buildindex -o $tmpdir/small1 -M100 ../chr901.fa >/dev/null 2>&1 
+subread-align -i $tmpdir/small1 -r data/test-noerror-r1.fq -o $tmpdir/test-tmp.sam1 -H -J >/dev/null 2>&1
+subread-align -u -i $tmpdir/small1 -r data/test-noerror-r1.fq -o $tmpdir/test-tmp.sam2 -H -J >/dev/null 2>&1
+subread-align -i $tmpdir/small1 -r data/test-noerror-r1.fq -R data/test-noerror-r2.fq -o $tmpdir/test-tmp.sam3 -H -J >/dev/null 2>&1
+subread-align -u -i $tmpdir/small1 -r data/test-noerror-r1.fq -R data/test-noerror-r2.fq -o $tmpdir/test-tmp.sam4  -Q -J >/dev/null 2>&1
+subread-align -i $tmpdir/small1 -r data/test-error-r1.fq -R data/test-error-r2.fq -o $tmpdir/test-tmp.sam5 -H -J >/dev/null 2>&1
+subread-align -i $tmpdir/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz -R data/test-err-mut-r2.fq.gz -o $tmpdir/test-tmp.sam6 -H -J --rg-id MyTestGroup --rg SM:sample1 --rg TP:1 --rg XX:YY >/dev/null 2>&1

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