add methods to extract column from record by its col. number

src/utils/FileRecordTools/Records/BamRecord.cpp

+/*
+ * BamRecord.cpp
+ *
+ *  Created on: Jan 14, 2014
+ *      Author: nek3d
+ */
+
 #include "BamRecord.h"
 #include "BamFileReader.h"
 #include "RecordKeyList.h"
@@ -15,143 +22,155 @@ BamRecord::~BamRecord()
 
 const BamRecord &BamRecord::operator=(const BamRecord &other)
 {
-	Bed6Interval::operator=(other);
-	_bamAlignment = other._bamAlignment;
-	return *this;
+        Bed6Interval::operator=(other);
+        _bamAlignment = other._bamAlignment;
+        return *this;
 }
 
 
 bool BamRecord::initFromFile(FileReader *fileReader)
 {
-	BamFileReader *bamFileReader = static_cast<BamFileReader*>(fileReader);
-	return initFromFile(bamFileReader);
+        BamFileReader *bamFileReader = static_cast<BamFileReader*>(fileReader);
+        return initFromFile(bamFileReader);
 
 }
 
 bool BamRecord::initFromFile(BamFileReader *bamFileReader)
 {
-	bamFileReader->getChrName(_chrName);
-
-	_bamChromId = bamFileReader->getCurrChromdId();
-	_startPos = bamFileReader->getStartPos();
-	int2str(_startPos, _startPosStr);
-	_endPos = bamFileReader->getEndPos();
-	int2str(_endPos, _endPosStr);
-	bamFileReader->getName(_name);
-	bamFileReader->getScore(_score);
-	char strandChar = bamFileReader->getStrand();
-	setStrand(strandChar);
-
-	_bamAlignment = bamFileReader->getAlignment();
-	_isUnmapped = !_bamAlignment.IsMapped();
-	_isMateUnmapped = !_bamAlignment.IsMateMapped();
-	return true;
+        bamFileReader->getChrName(_chrName);
+
+        _bamChromId = bamFileReader->getCurrChromdId();
+        _startPos = bamFileReader->getStartPos();
+        int2str(_startPos, _startPosStr);
+        _endPos = bamFileReader->getEndPos();
+        int2str(_endPos, _endPosStr);
+        bamFileReader->getName(_name);
+        bamFileReader->getScore(_score);
+        char strandChar = bamFileReader->getStrand();
+        setStrand(strandChar);
+
+        _bamAlignment = bamFileReader->getAlignment();
+        _isUnmapped = !_bamAlignment.IsMapped();
+        _isMateUnmapped = !_bamAlignment.IsMateMapped();
+        return true;
 }
 
 void BamRecord::clear()
 {
-	Bed6Interval::clear();
-	_bamChromId = -1;
-
-
-	//Clear the BamAlignment object. Sadly, it does not have a clear() method,
-	//so we have to do each member manually.
-	_bamAlignment.Name.clear();
-	_bamAlignment.Length = 0;
-	_bamAlignment.QueryBases.clear();
-	_bamAlignment.AlignedBases.clear();
-	_bamAlignment.Qualities.clear();
-	_bamAlignment.TagData.clear();
-	_bamAlignment.RefID = -1;
-	_bamAlignment.Position = -1;
-	_bamAlignment.Bin = 0;
-	_bamAlignment.MapQuality = 0;
-	_bamAlignment.AlignmentFlag = 0;
-	_bamAlignment.CigarData.clear();
-	_bamAlignment.MateRefID = -1;
-	_bamAlignment.MatePosition = -1;
-	_bamAlignment.InsertSize = -1;
-	_bamAlignment.Filename.clear();
-
-	_bamAlignment.SupportData.AllCharData.clear();
-	_bamAlignment.SupportData.BlockLength = 0;
-	_bamAlignment.SupportData.NumCigarOperations = 0;
-	_bamAlignment.SupportData.QueryNameLength = 0;
-	_bamAlignment.SupportData.QuerySequenceLength = 0;
-	_bamAlignment.SupportData.HasCoreOnly = false;
-
-	_bamAlignment.ErrorString.clear();
+        Bed6Interval::clear();
+        _bamChromId = -1;
+
+
+        //Clear the BamAlignment object. Sadly, it does not have a clear() method,
+        //so we have to do each member manually.
+        _bamAlignment.Name.clear();
+        _bamAlignment.Length = 0;
+        _bamAlignment.QueryBases.clear();
+        _bamAlignment.AlignedBases.clear();
+        _bamAlignment.Qualities.clear();
+        _bamAlignment.TagData.clear();
+        _bamAlignment.RefID = -1;
+        _bamAlignment.Position = -1;
+        _bamAlignment.Bin = 0;
+        _bamAlignment.MapQuality = 0;
+        _bamAlignment.AlignmentFlag = 0;
+        _bamAlignment.CigarData.clear();
+        _bamAlignment.MateRefID = -1;
+        _bamAlignment.MatePosition = -1;
+        _bamAlignment.InsertSize = -1;
+        _bamAlignment.Filename.clear();
+
+        _bamAlignment.SupportData.AllCharData.clear();
+        _bamAlignment.SupportData.BlockLength = 0;
+        _bamAlignment.SupportData.NumCigarOperations = 0;
+        _bamAlignment.SupportData.QueryNameLength = 0;
+        _bamAlignment.SupportData.QuerySequenceLength = 0;
+        _bamAlignment.SupportData.HasCoreOnly = false;
+
+        _bamAlignment.ErrorString.clear();
 
 
 }
 
 void BamRecord::print(QuickString &outBuf, RecordKeyList *keyList) const
 {
-	Bed6Interval::print(outBuf);
+        Bed6Interval::print(outBuf);
     printRemainingBamFields(outBuf, keyList);
 }
 
 void BamRecord::print(QuickString &outBuf, int start, int end, RecordKeyList *keyList) const
 {
-	Bed6Interval::print(outBuf, start, end);
+        Bed6Interval::print(outBuf, start, end);
     printRemainingBamFields(outBuf, keyList);
 }
 
 void BamRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyList *keyList) const
 {
-	Bed6Interval::print(outBuf, start, end);
+        Bed6Interval::print(outBuf, start, end);
     printRemainingBamFields(outBuf, keyList);
 }
 
 void BamRecord::printNull(QuickString &outBuf) const
 {
-	Bed6Interval::printNull(outBuf);
-	outBuf.append("\t.\t.\t.\t.\t.\t.", 12);
+        Bed6Interval::printNull(outBuf);
+        outBuf.append("\t.\t.\t.\t.\t.\t.", 12);
 }
 
 void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyList) const
 {
-	outBuf.append('\t');
-	outBuf.append(_bamAlignment.Position);
-	outBuf.append('\t');
-	outBuf.append(_endPos);
-	outBuf.append("\t0,0,0", 6);
-	outBuf.append('\t');
-
-	int numBlocks = (int)keyList->size();
-
-	if (numBlocks > 0) {
-		outBuf.append(numBlocks);
-
-		vector<int> blockLengths;
-		vector<int> blockStarts;
-		for (RecordKeyList::const_iterator_type iter = keyList->begin(); iter != keyList->end(); iter = keyList->next()) {
-			const Record *block = iter->value();
-			blockLengths.push_back(block->getEndPos() - block->getStartPos());
-			blockStarts.push_back(block->getStartPos() - _bamAlignment.Position);
-		}
-
-		outBuf.append('\t');
-		for (int i=0; i < (int)blockLengths.size(); i++) {
-			outBuf.append(blockLengths[i]);
-			outBuf.append(',');
-		}
-		outBuf.append('\t');
-		for (int i=0; i < (int)blockStarts.size(); i++) {
-			outBuf.append( blockStarts[i]);
-			outBuf.append(',');
-		}
-	}
-	else {
-		outBuf.append("1\t0,\t0,");
-	}
+        outBuf.append('\t');
+        outBuf.append(_bamAlignment.Position);
+        outBuf.append('\t');
+        outBuf.append(_endPos);
+        outBuf.append("\t0,0,0", 6);
+        outBuf.append('\t');
+
+        int numBlocks = (int)keyList->size();
+
+        if (numBlocks > 0) {
+                outBuf.append(numBlocks);
+
+                vector<int> blockLengths;
+                vector<int> blockStarts;
+                for (RecordKeyList::const_iterator_type iter = keyList->begin(); iter != keyList->end(); iter = keyList->next()) {
+                        const Record *block = iter->value();
+                        blockLengths.push_back(block->getEndPos() - block->getStartPos());
+                        blockStarts.push_back(block->getStartPos() - _bamAlignment.Position);
+                }
+
+                outBuf.append('\t');
+                for (int i=0; i < (int)blockLengths.size(); i++) {
+                        outBuf.append(blockLengths[i]);
+                        outBuf.append(',');
+                }
+                outBuf.append('\t');
+                for (int i=0; i < (int)blockStarts.size(); i++) {
+                        outBuf.append( blockStarts[i]);
+                        outBuf.append(',');
+                }
+        }
+        else {
+                outBuf.append("1\t0,\t0,");
+        }
 }
 
 void BamRecord::printUnmapped(QuickString &outBuf) const {
-	outBuf.append(_chrName.empty() ? "." : _chrName);
-	outBuf.append("\t-1\t-1\t");
-	outBuf.append(_name.empty() ? "." : _name);
-	outBuf.append('\t');
-	outBuf.append(_score.empty() ? "." : _score);
-	outBuf.append("\t.\t-1\t-1\t-1\t0,0,0\t0\t.\t."); // dot for strand, -1 for blockStarts and blockEnd
+        outBuf.append(_chrName.empty() ? "." : _chrName);
+        outBuf.append("\t-1\t-1\t");
+        outBuf.append(_name.empty() ? "." : _name);
+        outBuf.append('\t');
+        outBuf.append(_score.empty() ? "." : _score);
+        outBuf.append("\t.\t-1\t-1\t-1\t0,0,0\t0\t.\t."); // dot for strand, -1 for blockStarts and blockEnd
+}
+
+const QuickString &BamRecord::getField(int fieldNum) const
+{
+	//TBD: Determine what correct behavior should be.
+	//I.e. if users requests field 2, do they want Flag
+	//for Bam Records, or startPos for all records? -NEK 1/14/14.
+
+	return Bed6Interval::getField(fieldNum);
 }
+
+
+

src/utils/FileRecordTools/Records/BamRecord.h

@@ -38,6 +38,9 @@ public:
 	const BamTools::BamAlignment &getAlignment() const { return _bamAlignment; }
 	int getBamChromId() const { return _bamChromId; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return 12; }
+
 protected:
 	BamTools::BamAlignment _bamAlignment;
 	int _bamChromId; //different from chromId, because BAM file may be in different order

src/utils/FileRecordTools/Records/Bed3Interval.cpp

@@ -61,3 +61,21 @@ void Bed3Interval::print(QuickString &outBuf, const QuickString & start, const Q
 void Bed3Interval::printNull(QuickString &outBuf) const {
 	outBuf.append(".\t-1\t-1", 7);
 }
+
+const QuickString &Bed3Interval::getField(int fieldNum) const
+{
+	switch (fieldNum) {
+	case 1:
+		return _chrName;
+		break;
+	case 2:
+		return _startPosStr;
+		break;
+	case 3:
+		return _endPosStr;
+		break;
+	default:
+		return Record::getField(fieldNum);
+		break;
+	}
+}

src/utils/FileRecordTools/Records/Bed3Interval.h

@@ -29,6 +29,9 @@ public:
 	virtual void printNull(QuickString &outBuf) const;
 	virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED3_RECORD_TYPE; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return 3; }
+
 protected:
 	virtual ~Bed3Interval();
 

src/utils/FileRecordTools/Records/Bed4Interval.cpp

@@ -48,3 +48,15 @@ void Bed4Interval::printNull(QuickString &outBuf) const
 	outBuf.append("\t.", 2);
 }
 
+const QuickString &Bed4Interval::getField(int fieldNum) const
+{
+	switch (fieldNum) {
+	case 4:
+		return _name;
+		break;
+	default:
+		return Bed3Interval::getField(fieldNum);
+		break;
+	}
+}
+

src/utils/FileRecordTools/Records/Bed4Interval.h

@@ -26,6 +26,10 @@ public:
 	virtual void printNull(QuickString &outBuf) const;
 	virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED4_RECORD_TYPE; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return 4; }
+
+
 protected:
 	virtual ~Bed4Interval();
 };

src/utils/FileRecordTools/Records/Bed5Interval.cpp

@@ -55,3 +55,18 @@ void Bed5Interval::printNull(QuickString &outBuf) const
 	outBuf.append("\t.\t-1", 5);
 }
 
+const QuickString &Bed5Interval::getField(int fieldNum) const
+{
+	switch (fieldNum) {
+	case 4:
+		return _name;
+		break;
+	case 5:
+		return _score;
+		break;
+
+	default:
+		return Bed3Interval::getField(fieldNum);
+		break;
+	}
+}

src/utils/FileRecordTools/Records/Bed5Interval.h

@@ -25,6 +25,10 @@ public:
 	virtual void printNull(QuickString &outBuf) const;
 	virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED5_RECORD_TYPE; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return 5; }
+
+
 protected:
 	virtual ~Bed5Interval();
 };

src/utils/FileRecordTools/Records/Bed6Interval.cpp

@@ -64,3 +64,20 @@ void Bed6Interval::printNull(QuickString &outBuf) const
 	outBuf.append("\t.\t-1\t.", 7);
 }
 
+const QuickString &Bed6Interval::getField(int fieldNum) const
+{
+	switch (fieldNum) {
+	case 4:
+		return _name;
+		break;
+	case 5:
+		return _score;
+		break;
+	case 6:
+		return _strand;
+		break;
+	default:
+		return Bed3Interval::getField(fieldNum);
+		break;
+	}
+}

src/utils/FileRecordTools/Records/Bed6Interval.h

@@ -25,6 +25,10 @@ public:
 	virtual void printNull(QuickString &outBuf) const;
 	virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED6_RECORD_TYPE; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return 6; }
+
+
 protected:
 	virtual ~Bed6Interval();
 };

src/utils/FileRecordTools/Records/BedGraphInterval.cpp

@@ -48,3 +48,15 @@ void BedGraphInterval::printNull(QuickString &outBuf) const
 	outBuf.append("\t.", 2);
 }
 
+const QuickString &BedGraphInterval::getField(int fieldNum) const
+{
+	switch (fieldNum) {
+	case 4:
+		return _name;
+		break;
+	default:
+		return Bed3Interval::getField(fieldNum);
+		break;
+	}
+}
+

src/utils/FileRecordTools/Records/BedGraphInterval.h

@@ -25,6 +25,10 @@ public:
 	virtual void printNull(QuickString &outBuf) const;
 	virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return 4; }
+
+
 protected:
 	virtual ~BedGraphInterval();
 };

src/utils/FileRecordTools/Records/BedPlusInterval.cpp

@@ -105,36 +105,15 @@ void BedPlusInterval::printNull(QuickString &outBuf) const
 	for (int i=startOtherIdx; i < _numPrintFields; i++) {
 		outBuf.append("\t.");
 	}
-
 }
 
-QuickString BedPlusInterval::getField(int fieldNum) const
+const QuickString &BedPlusInterval::getField(int fieldNum) const
 {
 	//a request for any of the first six fields will retrieve
 	//chrom, start, end, name, score, and strand, in that order.
 	//A request for field 6+ will go to the otherIdxs.
-
-	switch (fieldNum) {
-	case 0:
-		return _chrName;
-		break; //redundant after a return, but good practice anyway.
-	case 1:
-		return _startPosStr;
-		break;
-	case 2:
-		return _endPosStr;
-		break;
-	case 3:
-		return _name;
-		break;
-	case 4:
-		return _score;
-		break;
-	case 5:
-		return _strand;
-		break;
-	default:
-		return (*(_otherIdxs[fieldNum - startOtherIdx]));
-		break;
+	if (fieldNum > startOtherIdx && fieldNum <= startOtherIdx + (int)_otherIdxs.size()) {
+		return (*(_otherIdxs[fieldNum - startOtherIdx - 1]));
 	}
+	return Bed6Interval::getField(fieldNum);
 }

src/utils/FileRecordTools/Records/BedPlusInterval.h

@@ -30,7 +30,9 @@ public:
 	//if the number of fields frequently differ between this object and the one being copied.
 	const BedPlusInterval &operator=(const BedPlusInterval &other);
 
-	virtual QuickString getField(int fieldNum) const;
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  { return startOtherIdx + _otherIdxs.size(); }
+
 	virtual void setField(int fieldNum, const QuickString &str) { (*(_otherIdxs[fieldNum])) = str; }
 	virtual void setField(int fieldNum, const string &str) { (*(_otherIdxs[fieldNum])) = str; }
 	virtual void setField(int fieldNum, const char *str) { (*(_otherIdxs[fieldNum])) = str; }

src/utils/FileRecordTools/Records/Record.cpp

@@ -192,3 +192,17 @@ ostream &operator << (ostream &out, const Record &record)
 	out << errBuf;
 	return out;
 }
+
+const QuickString &Record::getField(int fieldNum) const
+{
+//    try {
+//        _column_vec.push_back(hits[i].fields.at(_column));
+//    }
+//    catch(std::out_of_range& e) {
+        cerr << endl << "*****" << endl
+             << "*****ERROR: requested column " << fieldNum <<
+             " , but record only has fields 1 - " << getNumFields() << ". Exiting." << endl
+              << endl << "*****" << endl;
+        exit(1);
+//    }
+}

src/utils/FileRecordTools/Records/Record.h

@@ -82,6 +82,9 @@ public:
 	virtual void setScore(const string &chr) { _score = chr; }
 	virtual void setScore(const char *chr) { _score = chr; }
 
+	virtual const QuickString &getField(int fieldNum) const;
+	virtual int getNumFields() const  = 0;
+
 	virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::UNKNOWN_RECORD_TYPE; }
 
 	virtual bool coordsValid(); //test that no coords negative, end not less than start, check zeroLength (see below).