Fixed bug133, missing intersection of zero length records

src/utils/Contexts/ContextBase.cpp

@@ -32,7 +32,7 @@ ContextBase::ContextBase()
   _writeOverlap(false),
   _writeAllOverlap(false),
   _haveFraction(false),
-  _overlapFraction(1E-9),
+  _overlapFraction(0.0),
   _reciprocal(false),
   _sameStrand(false),
   _diffStrand(false),

src/utils/FileRecordTools/Records/Record.cpp

@@ -160,15 +160,27 @@ bool Record::sameChromIntersects(const Record *record,
 	int otherStart = record->getStartPos();
 	int otherEnd = record->getEndPos();
 
+	bool otherZeroLen = (otherStart - otherEnd == 0);
 	int maxStart = max(_startPos, otherStart);
 	int minEnd = min(_endPos, otherEnd);
 
+	bool localZeroLen = (_endPos - _startPos == 0);
 	//rule out all cases of no intersection at all
 	if (minEnd < maxStart) {
 		return false;
 	}
 
 
+	if (overlapFraction == 0.0) {
+		//don't care about amount of overlap.
+		//however, if minEnd and maxStart are equal, and
+		//neither record is zeroLen, return false.
+		if (minEnd == maxStart && !otherZeroLen && !localZeroLen) {
+			return false;
+		}
+		return true;
+	}
+
 	int overlapBases = minEnd - maxStart;
 	int len = _endPos - _startPos;
 	int otherLen = otherEnd - otherStart;

src/utils/RecordOutputMgr/RecordOutputMgr.cpp

@@ -210,6 +210,7 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 				if ((static_cast<ContextIntersect *>(_context))->getWriteAllOverlap()) {
 					// -wao the user wants to force the reporting of 0 overlap
 					if (printKeyAndTerminate(keyList)) {
+
 						_currBamBlockList = NULL;
 						return;
 					}
@@ -223,6 +224,7 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 				else if ((static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
 					if (printKeyAndTerminate(keyList)) {
 						_currBamBlockList = NULL;
+
 						return;
 					}
 					tab();
@@ -230,11 +232,13 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 					newline();
 					if (needsFlush()) flush();
 					_currBamBlockList = NULL;
+
 					return;
 				}
 			} else {
 				if (printBamRecord(keyList, true) == BAM_AS_BAM) {
 					_currBamBlockList = NULL;
+
 					return;
 				}
 				int hitIdx = 0;
@@ -252,14 +256,17 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
 			newline();
 		}
 		_currBamBlockList = NULL;
+
 		return;
 	} else if (_context->getProgram() == ContextBase::MAP) {
 		printKeyAndTerminate(keyList);
 		_currBamBlockList = NULL;
+
 		return;
 	} else if (_context->getProgram() == ContextBase::MERGE) {
 		printKeyAndTerminate(keyList);
 		_currBamBlockList = NULL;
+
 		return;
 	}
 }
@@ -380,6 +387,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
 		newline();
 		if (needsFlush()) flush();
 	}
+	const_cast<Record *>(keyRecord)->adjustZeroLength();
 }
 
 void RecordOutputMgr::reportOverlapSummary(RecordKeyVector &keyList)

test/intersect/a_testZeroLen.bed

+chr1	5	15	r1
+chr1	7	12	r3
+chr1	20	25	r2

test/intersect/b_testZeroLen.bed

+chr1	9	9	m3
+chr1	50	150	m1
+chr2	20	25	m2

test/intersect/new_test-intersect.sh

@@ -764,3 +764,24 @@ $BT intersect -a oneRecordNoNewline.bed -b oneRecordNoNewline.bed > obs
 check obs exp
 rm obs exp
 
+###########################################################
+#  Test zero length intersections in non-bam files.
+############################################################
+echo "    intersect.new.t65...\c"
+echo \
+"chr1	5	15	r1	chr1	9	9	m3	0
+chr1	7	12	r3	chr1	9	9	m3	0" > exp
+$BT intersect -a a_testZeroLen.bed -b b_testZeroLen.bed -wo > obs
+check exp obs
+rm exp obs
+
+###########################################################
+#  Test zero length intersections in non-bam files, -sorted
+############################################################
+echo "    intersect.new.t66...\c"
+echo \
+"chr1	5	15	r1	chr1	9	9	m3	0
+chr1	7	12	r3	chr1	9	9	m3	0" > exp
+$BT intersect -a a_testZeroLen.bed -b b_testZeroLen.bed -wo -sorted> obs
+check exp obs
+rm exp obs