From 6cf8042a36cc7a6412ae009096af25c267306be5 Mon Sep 17 00:00:00 2001
From: Michael Hiller <hiller@mpi-cbg.de>
Date: Sat, 1 Apr 2017 11:47:47 +0200
Subject: [PATCH] added tests.sh to run a few standardized tests

---
 extra/samples/sample4.out |  2 +-
 extra/samples/sample5.in  |  2 +-
 extra/samples/sample5.out |  4 ++--
 tests.sh                  | 25 +++++++++++++++++++++++++
 4 files changed, 29 insertions(+), 4 deletions(-)
 create mode 100755 tests.sh

diff --git a/extra/samples/sample4.out b/extra/samples/sample4.out
index 2a31299..def6d95 100644
--- a/extra/samples/sample4.out
+++ b/extra/samples/sample4.out
@@ -1,4 +1,4 @@
 >referenceExon
                       aaCCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
 >query
-cttccccatttttatctcatagac------------------------------------------------------------------------------------------CCC------------
+cttccccatttttatctcatagac------------------------------------------------------------------------CCC------------------------------
diff --git a/extra/samples/sample5.in b/extra/samples/sample5.in
index 88deb8c..7c53b0a 100644
--- a/extra/samples/sample5.in
+++ b/extra/samples/sample5.in
@@ -1,4 +1,4 @@
 >referenceExon
-                      aaCCTAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
+                      aaCCTAAACCCAAACCCAAACCC
 >query
 cttccccatttttatctcatagacCCT
diff --git a/extra/samples/sample5.out b/extra/samples/sample5.out
index e8ff643..329acea 100644
--- a/extra/samples/sample5.out
+++ b/extra/samples/sample5.out
@@ -1,4 +1,4 @@
 >referenceExon
-                      aaCCTAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCC
+                      aaCCTAAACCCAAACCCAAACCC
 >query
-cttccccatttttatctcatagacCCT------------------------------------------------------------------------------------------------------
+cttccccatttttatctcatagacCCT------------------
diff --git a/tests.sh b/tests.sh
new file mode 100755
index 0000000..b4adb97
--- /dev/null
+++ b/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