diff --git a/src/sampleFile/SampleFile.cpp b/src/sampleFile/SampleFile.cpp
index 2c4c1a7d90ff17cba7c23413d4b5e95ba6fb4dc9..8f532c5f47a8eb89da81fac4d5c3a35f15a17187 100644
--- a/src/sampleFile/SampleFile.cpp
+++ b/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;
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.cpp b/src/utils/FileRecordTools/Records/Bed6Interval.cpp
index 0f9e7ea4183981acf281156e5dd85fe88edd10cd..b486333a66757b4d36896c273d0d46d9798e9ab6 100644
--- a/src/utils/FileRecordTools/Records/Bed6Interval.cpp
+++ b/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);
}
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp b/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
index f062075361957ba655a84218ecc69b183697d724..d3e0c01ad9df1ac218cc15c310affba359e0d199 100644
--- a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
+++ b/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]));
diff --git a/src/utils/FileRecordTools/Records/GffRecord.cpp b/src/utils/FileRecordTools/Records/GffRecord.cpp
index cceb01ac140e37372bf039bb55e99256f1159418..f13c8fd8c59f357eaefb4136ddb5a1a4fa8d72cb 100644
--- a/src/utils/FileRecordTools/Records/GffRecord.cpp
+++ b/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) {
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index cb5e5f445480c0f8eb57481f5fa753e84c04ebf8..6bad45dd232c6e06db3fa169986518d640538188 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/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.
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 9f80a960d6aba491d5f050c20c8a52153c5350fe..92df4bad97dadde7e8a9e6b1d6d4b0dacd88dad0 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/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;