Fixed bug262: stranded map with BedPlus

src/utils/FileRecordTools/Records/BedPlusInterval.cpp

@@ -70,6 +70,13 @@ const QuickString &BedPlusInterval::getField(int fieldNum) const
 {
 	if (fieldNum > _numFixedFields) {
 		return _plusFields.getField(fieldNum);
+	} else if (fieldNum == 4 && _numFixedFields >=4) {
+		return _name;
+	} else if (fieldNum == 5 && _numFixedFields >=5) {
+		return _score;
+	}
+	else if (fieldNum == 6 && _numFixedFields >=6) {
+		return _strand;
 	}
 	return Bed3Interval::getField(fieldNum);
 }

src/utils/FileRecordTools/Records/VcfRecord.h

@@ -31,6 +31,7 @@ public:
 protected:
 	QuickString _varRef;
 	QuickString _varAlt;
+	static const int numFixedFields = 6;
 
 	void printOtherFields(QuickString &outBuf) const;
 };

test/map/bug262_a.bed

+1	3215742	3216021	.	0	-
+1	3217007	3218115	.	0	-

test/map/bug262_b.bed

+1	3215742	3216021	.	1	-	0	0	3
+1	3217007	3218115	.	1	-	0	0	1

test/map/test-map.sh

@@ -808,3 +808,32 @@ chr1	15000	20000	11.44444444" > exp
 $BT map -a d.bed -b fullFields.bam -c 5 -o mean > obs
 check exp obs
 rm exp obs
+
+
+###########################################################
+#  Bug 262: Test stranded map with BedPlus records. 
+# -s (lowercase) should give results
+############################################################
+echo "    map.t54...\c"
+echo \
+"1	3215742	3216021	.	0	-	1
+1	3217007	3218115	.	0	-	1" > exp
+$BT map -a bug262_a.bed -b bug262_b.bed -s > obs
+check exp obs
+rm exp obs
+
+
+###########################################################
+#  Bug 262: Test stranded map with BedPlus records. 
+# -S (uppercase) should NOT give results
+############################################################
+echo "    map.t55...\c"
+echo \
+"1	3215742	3216021	.	0	-	.
+1	3217007	3218115	.	0	-	." > exp
+$BT map -a bug262_a.bed -b bug262_b.bed -S > obs
+check exp obs
+rm exp obs
+
+
+