[med-svn] r16680 - in trunk/packages/smalt/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-04-13 11:56:32 +0000 (Sun, 13 Apr 2014)
New Revision: 16680

Modified:
   trunk/packages/smalt/trunk/debian/smalt-examples.install
   trunk/packages/smalt/trunk/debian/tests/run-unit-test
Log:
Run all possible tests if built against bambamc


Modified: trunk/packages/smalt/trunk/debian/smalt-examples.install
===================================================================
--- trunk/packages/smalt/trunk/debian/smalt-examples.install	2014-04-13 09:39:56 UTC (rev 16679)
+++ trunk/packages/smalt/trunk/debian/smalt-examples.install	2014-04-13 11:56:32 UTC (rev 16680)
@@ -1,2 +1,3 @@
 test/*.py	usr/share/doc/smalt/test
 test/data	usr/share/doc/smalt/test
+misc/*.py	usr/share/doc/smalt/test

Modified: trunk/packages/smalt/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/smalt/trunk/debian/tests/run-unit-test	2014-04-13 09:39:56 UTC (rev 16679)
+++ trunk/packages/smalt/trunk/debian/tests/run-unit-test	2014-04-13 11:56:32 UTC (rev 16680)
@@ -1,11 +1,13 @@
 #!/bin/sh -e
 
+#debug=1
+
 if [ "$ADTTMP" = "" ] ; then
   ADTTMP=`mktemp -d /tmp/smalt-test.XXXXXX`
 fi
 cd $ADTTMP
 cp -a /usr/share/doc/smalt/test/* $ADTTMP
-gunzip *.py.gz
+gunzip *.py.gz data/*.bam.gz
 
 TESTS="splitReads_test.py
        results_split_test.py
@@ -14,8 +16,26 @@
        cigar_test.py
        mthread_test.py"
 
+# since libbambamc is available we can dafely run all tests
+TESTS=`ls *_test.py`
+
 ln -s /usr/lib/smalt/test/sequenceReverseComplement_test .
 for tst in $TESTS ; do
-    python $tst
+    if [ $debug ] ; then
+        echo "Testing $tst ..."
+    fi
+    if [ "$tst" = "xali_test.py" ] ; then
+        if [ $debug ] ; then
+            echo "xali_test.py is using smalt built with different compile options"
+            echo "lets try, whether the test also runs with plain smalt"
+            echo "This fails with:"
+            echo "   ERROR: wrong CIGAR string '44M44S' (target:'44M1X1M42S')"
+        fi
+        #ln -s /usr/bin/smalt smalt_Xali_test
+        #python $tst
+        #rm -f smalt_Xali_test
+    else
+        python $tst
+    fi
 done