Merge branch 'google_test'

Makefile

@@ -109,3 +109,8 @@ clean:
 	@rm -Rf $(BT_ROOT)/include
 
 .PHONY: clean
+
+test: all
+	@cd test; sh test.sh
+
+.PHONY: test

src/shuffleBed/shuffleBed.cpp

@@ -81,13 +81,12 @@ BedShuffle::~BedShuffle(void) {
 
 
 void BedShuffle::Shuffle() {
-    BED bedEntry, nullBed;     // used to store the current BED line from the BED file.
+    BED bedEntry;
     _bed->Open();
     while (_bed->GetNextBed(bedEntry)) {
         if (_bed->_status == BED_VALID) {
             ChooseLocus(bedEntry);
             _bed->reportBedNewLine(bedEntry);
-            bedEntry = nullBed;
         }
     }
     _bed->Close();
@@ -97,8 +96,7 @@ void BedShuffle::Shuffle() {
 
 void BedShuffle::ShuffleWithExclusions() {
 
-    BED bedEntry, nullBed;     // used to store the current BED line from the BED file.
-
+    BED bedEntry;
     _bed->Open();
     while (_bed->GetNextBed(bedEntry)) {
         if (_bed->_status == BED_VALID) {
@@ -124,7 +122,6 @@ void BedShuffle::ShuffleWithExclusions() {
                 _bed->reportBedNewLine(bedEntry);
             }
         }
-        bedEntry = nullBed;
     }
     _bed->Close();
 }

test/intersect/a.bed

+chr1	10	20
+chr1	30	40

test/intersect/intersect.t1.exp

+chr1	10	20
+chr1	30	40

test/intersect/obs

+chr1	10	20
+chr1	30	40

test/intersect/test-intersect.sh

+check()
+{
+	if diff $1 $2; then
+    	echo ok
+	else
+    	echo fail
+	fi
+}
+
+echo "    intersect.t1 self intersect...\c"
+../../bin/bedtools intersect -a a.bed -b a.bed > obs
+check obs intersect.t1.exp

test/merge/a.bed

+chr1	10	20
+chr1	30	40
+chr1	40	50
+chr1	45	100
+

test/merge/a.names.bed

+chr1	10	20	a1
+chr1	30	40	a2
+chr1	40	50	a3
+chr1	45	100	a4

test/merge/test-merge.sh

+BT=../../bin/bedtools
+
+check()
+{
+	if diff $1 $2; then
+    	echo ok
+		return 1
+	else
+    	echo fail
+		return 0
+	fi
+}
+
+# cat a.bed
+# chr1	10	20
+# chr1	30	40
+# chr1	40	50
+# chr1	45	100
+
+###########################################################
+# Test #1
+#  Test a basic merge; one interval should be un-merged, 
+#  the other two should be merged.
+###########################################################
+echo "    merge.t1...\c"
+echo \
+"chr1	10	20
+chr1	30	100" > exp
+$BT merge -i a.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test #2
+#  Enforce coordinate sorted input.
+###########################################################
+echo "    merge.t2...\c"
+tac a.bed | $BT merge -i - 2> obs
+echo "ERROR: input file: (-) is not sorted by chrom then start.
+       The start coordinate at line 3 is less than the start at line 2" > exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test #3
+#  Test the counting of merged intervals. (-n)
+###########################################################
+echo "    merge.t3...\c"
+echo \
+"chr1	10	20	1
+chr1	30	100	3" > exp
+$BT merge -i a.bed -n > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test #4
+#  Test the listing of names from merged intervals. (-nms)
+#  a.bed should fail, as there is no name field
+###########################################################
+echo "    merge.t4...\c"
+echo \
+"chr1	10	20
+*****
+*****ERROR: No names found to report for the -names option. Exiting.
+*****" > exp
+$BT merge -i a.bed -nms &> obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test #5
+#  Test the listing of names from merged intervals. (-nms)
+#  a.named.bed should work, as there are name fields
+#  
+# cat a.names.bed
+# chr1	10	20	a1
+# chr1	30	40	a2
+# chr1	40	50	a3
+# chr1	45	100	a4
+###########################################################
+echo "    merge.t5...\c"
+echo \
+"chr1	10	20	a1
+chr1	30	100	a2;a3;a4" > exp
+$BT merge -i a.names.bed -nms > obs
+check obs exp
+rm obs exp
\ No newline at end of file

test/test.sh

+echo " Testing bedtools intersect:"
+cd intersect
+sh test-intersect.sh
+cd ..
+
+echo " Testing bedtools merge:"
+cd merge
+sh test-merge.sh
+cd ..
\ No newline at end of file