Adds a test example and functional testing. Fixes #4

.gitignore

@@ -5,3 +5,4 @@ rp-files/
 testdata/
 *.o
 *~
+tests/chr*

Makefile

@@ -23,9 +23,14 @@ CXXFLAGS+=-O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0
 
 all: chopBAI
 
-chopBAI: chopBAI.o 
+chopBAI: chopBAI.o
 
 chopBAI.o: chopBAI.cpp bam_index_csi.h
 
+test:
+		cd tests/ && ./alltests.sh
+
 clean:
 	rm -f *.o chopBAI
+
+.PHONY: test

tests/alltests.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# Test all options
+for opts in "" "--linear" "--symlink" "--linear --symlink"; do
+  echo "Testing chopBAI with option $opts"
+
+
+  for chr in chrA:B:C:D chrA:B chrB; do
+    echo "  Testing chromosome $chr"
+    ./test.sh $chr $opts
+    for reg in "100" "2,000" "1-100" "1,000-10,000"; do
+      chrreg="${chr}:${reg}"
+      ./test.sh $chrreg $opts
+    done
+  done
+done

tests/test.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+set -eo pipefail
+
+REGION=$1
+#clean up directory if it exists
+if [[ -d "${REGION}" ]]; then
+  rm -rf ./${REGION}
+fi
+
+shift 1
+OPTS=$@
+echo "Running command: ../chopBAI ${OPTS} test.sorted.bam ${REGION}"
+../chopBAI ${OPTS} test.sorted.bam ${REGION}
+
+if [[ -d ${REGION} ]]; then
+  #ok, directory exists
+  cd ${REGION}
+  if [[ ! -f test.sorted.bam ]]; then
+    if [[ $OPTS =~ "--symlink" || $OPTS =~ "-s" ]]; then
+      echo "Symlink not created!"
+      exit 1
+    else
+      #we'll just create it ourselves
+      ln -s ../test.sorted.bam
+    fi
+
+    samtools view test.sorted.bam ${REGION} > out.chopBAI.sam
+    samtools view ../test.sorted.bam ${REGION} > out.samtools.sam
+    diff -q  out.chopBAI.sam out.samtools.sam
+  fi
+else
+  echo "Directory ${REGION} was not created."
+  exit 1
+fi