added tests.sh to run a few standardized tests

extra/samples/sample4.out

@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
 >query
-cttccccatttttatctcatagac------------------------------------------------------------------------------------------CCC------------
+cttccccatttttatctcatagac------------------------------------------------------------------------CCC------------------------------

extra/samples/sample5.in

@@ -1,4 +1,4 @@
 >referenceExon
-                      aaCCTAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
+                      aaCCTAAACCCAAACCCAAACCC
 >query
 cttccccatttttatctcatagacCCT

extra/samples/sample5.out

@@ -1,4 +1,4 @@
 >referenceExon
-                      aaCCTAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
+                      aaCCTAAACCCAAACCCAAACCC
 >query
-cttccccatttttatctcatagacCCT------------------------------------------------------------------------------------------------------
+cttccccatttttatctcatagacCCT------------------

tests.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+if [ $# -ne 1 ]; then
+  echo "Usage: $0 ./cesar"
+  exit 1
+fi
+
+set -e
+
+HERE=$(dirname $0)
+cesar=$1
+
+# check if cesar successfully returns the test samples.
+
+echo "Checking for correct behaviour."
+for f in $(find $HERE/extra/samples -name '*.in'); do
+  diff -q <($cesar $f) $HERE/extra/samples/$(basename $f .in).out
+  if [ $? -ne 0 ]; then
+    echo "$f... NOK"
+    exit 1
+  else
+    echo "$f... OK"
+  fi
+done
+exit 0