Changed handling of strand in records to allow non-strand strings in sixth field of records.

src/sampleFile/SampleFile.cpp

@@ -120,10 +120,10 @@ bool SampleFile::strandComplies(const Record * record) {
 	if (!_context->getSameStrand()) {
 		return true;
 	}
-	if (_context->getForwardOnly() && record->getStrand() == Record::FORWARD) {
+	if (_context->getForwardOnly() && record->getStrandVal() == Record::FORWARD) {
 		return true;
 	}
-	if (_context->getReverseOnly() && record->getStrand() == Record::REVERSE) {
+	if (_context->getReverseOnly() && record->getStrandVal() == Record::REVERSE) {
 		return true;
 	}
 	return false;

src/utils/FileRecordTools/Records/Bed6Interval.cpp

@@ -18,10 +18,8 @@ bool Bed6Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
 
 	fileReader->getField(3, _name);
 	fileReader->getField(4, _score);
-	char strandChar = 0;
-	fileReader->getField(5, strandChar);
-	setStrand(strandChar);
-
+	fileReader->getField(5, _strand);
+	adjustStrandVal();
 	return baseRetFlag;
 }
 
@@ -34,7 +32,7 @@ void Bed6Interval::print(QuickString &outBuf) const
 	outBuf.append('\t');
 	outBuf.append(_score);
 	outBuf.append('\t');
-	outBuf.append(getStrandChar());
+	outBuf.append(_strand);
 }
 
 void Bed6Interval::print(QuickString &outBuf, int start, int end) const
@@ -45,7 +43,7 @@ void Bed6Interval::print(QuickString &outBuf, int start, int end) const
 	outBuf.append('\t');
 	outBuf.append(_score);
 	outBuf.append('\t');
-	outBuf.append(getStrandChar());
+	outBuf.append(_strand);
 }
 
 void Bed6Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
@@ -56,7 +54,7 @@ void Bed6Interval::print(QuickString &outBuf, const QuickString & start, const Q
 	outBuf.append('\t');
 	outBuf.append(_score);
 	outBuf.append('\t');
-	outBuf.append(getStrandChar());
+	outBuf.append(_strand);
 }
 
 

src/utils/FileRecordTools/Records/BedPlusInterval.cpp

@@ -114,19 +114,15 @@ QuickString BedPlusInterval::getField(int fieldNum) const
 	//chrom, start, end, name, score, and strand, in that order.
 	//A request for field 6+ will go to the otherIdxs.
 
-	QuickString buffer;
-
 	switch (fieldNum) {
 	case 0:
 		return _chrName;
 		break; //redundant after a return, but good practice anyway.
 	case 1:
-		int2str(_startPos, buffer);
-		return buffer;
+		return _startPosStr;
 		break;
 	case 2:
-		int2str(_endPos, buffer);
-		return buffer;
+		return _endPosStr;
 		break;
 	case 3:
 		return _name;
@@ -135,8 +131,7 @@ QuickString BedPlusInterval::getField(int fieldNum) const
 		return _score;
 		break;
 	case 5:
-		buffer.append(getStrandChar());
-		return buffer;
+		return _strand;
 		break;
 	default:
 		return (*(_otherIdxs[fieldNum - startOtherIdx]));

src/utils/FileRecordTools/Records/GffRecord.cpp

@@ -38,9 +38,8 @@ bool GffRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
 	fileReader->getField(5, _score);
 
 	//GFF allows a '.' for the strandChar, signifying it is not known.
-	char strandChar = 0;
-	fileReader->getField(6, strandChar);
-	setStrand(strandChar);
+	fileReader->getField(6, _strand);
+	adjustStrandVal();
 
 	fileReader->getField(7, _frame);
 	_numFields = fileReader->getNumFields();
@@ -104,7 +103,7 @@ void GffRecord::printRemainingFields(QuickString &outBuf) const
 {
 	outBuf.append(_score);
 	outBuf.append('\t');
-	outBuf.append(getStrandChar());
+	outBuf.append(_strand);
 	outBuf.append('\t');
 	outBuf.append(_frame);
 	if (_numFields == 9) {

src/utils/FileRecordTools/Records/Record.cpp

@@ -6,7 +6,7 @@ Record::Record()
 : _chrId(-1),
   _startPos(-1),
   _endPos(-1),
-  _strand(UNKNOWN),
+  _strandVal(UNKNOWN),
   _zeroLength(false),
   _isUnmapped(false),
   _isMateUnmapped(false)
@@ -23,6 +23,7 @@ const Record &Record::operator=(const Record &other)
 	_startPos = other._startPos;
 	_endPos = other._endPos;
 	_strand = other._strand;
+	_strandVal = other._strandVal;
 	_name = other._name;
 	return *this;
 }
@@ -34,7 +35,8 @@ void Record::clear() {
 	_endPos = -1;
 	_name.clear();
 	_score.clear();
-	_strand = UNKNOWN;
+	_strand.clear();
+	_strandVal = UNKNOWN;
 	_startPosStr.clear();
 	_endPosStr.clear();
 	_zeroLength = false;
@@ -42,37 +44,6 @@ void Record::clear() {
 	_isMateUnmapped = false;
 }
 
-void Record::setStrand(char val)
-{
-	switch (val) {
-	case '+':
-		_strand = FORWARD;
-		break;
-	case '-':
-		_strand = REVERSE;
-		break;
-	default:
-		_strand = UNKNOWN;
-		break;
-	}
-}
-
-char Record::getStrandChar() const
-{
-	switch (_strand) {
-	case FORWARD:
-		return '+';
-		break;
-	case REVERSE:
-		return '-';
-		break;
-	case UNKNOWN:
-	default:
-		return '.';
-	}
-//	return '.';
-}
-
 bool Record::operator < (const Record &other) const
 {
 
@@ -144,8 +115,8 @@ bool Record::sameChromIntersects(const Record *record,
 	//rule out different strandedness first.
 	//If the strand is unknown in either case, then queries regarding strandedness
 	//can not be answered, so we return false;
-	bool isSameStrand = (_strand == record->_strand && _strand != UNKNOWN);
-	bool isDiffStrand = ( _strand != UNKNOWN && record->_strand != UNKNOWN && _strand != record->_strand);
+	bool isSameStrand = (_strandVal == record->_strandVal && _strandVal != UNKNOWN);
+	bool isDiffStrand = ( _strandVal != UNKNOWN && record->_strandVal != UNKNOWN && _strandVal != record->_strandVal);
 
 	if (wantSameStrand && !isSameStrand) {
 		return false; //want same, but they're not same.

src/utils/FileRecordTools/Records/Record.h

@@ -59,10 +59,18 @@ public:
 	virtual bool getZeroLength() const { return _zeroLength; }
 	virtual void setZeroLength(bool val) { _zeroLength = val; }
 
-	virtual strandType getStrand() const { return _strand; }
-	virtual void setStrand(strandType val) { _strand = val; }
-	virtual void setStrand(char val);
-	virtual char getStrandChar() const;
+	virtual const QuickString &getStrand() const { return _strand; }
+	virtual void setStrand(const QuickString &val) { _strand = val;
+		_strandVal = (val == "+" ? FORWARD : (val == "-" ? REVERSE : UNKNOWN));
+	}
+	virtual void setStrand(char val) { _strand = val;
+		_strandVal = (val == '+' ? FORWARD : (val == '-' ? REVERSE : UNKNOWN));
+	}
+	virtual void adjustStrandVal() {
+		_strandVal = (_strand == "+" ? FORWARD : (_strand == "-" ? REVERSE : UNKNOWN));
+	}
+
+	virtual strandType getStrandVal() const {return _strandVal; }
 
 	virtual const QuickString &getName() const { return _name; }
 	virtual void setName(const QuickString &chr) { _name = chr; }
@@ -132,7 +140,8 @@ protected:
 	QuickString _endPosStr;
 	QuickString _name;
 	QuickString _score;
-	strandType _strand;
+	QuickString _strand;
+	strandType _strandVal;
 	bool _zeroLength;
 	bool _isUnmapped;
 	bool _isMateUnmapped;