From 61b7a97626bc8a535fc2a5953f758b19926a0766 Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Sat, 1 Feb 2014 16:35:47 -0500
Subject: [PATCH] add methods to extract column from record by its col. number
---
.../FileRecordTools/Records/BamRecord.cpp | 213 ++++++++++--------
src/utils/FileRecordTools/Records/BamRecord.h | 3 +
.../FileRecordTools/Records/Bed3Interval.cpp | 18 ++
.../FileRecordTools/Records/Bed3Interval.h | 3 +
.../FileRecordTools/Records/Bed4Interval.cpp | 12 +
.../FileRecordTools/Records/Bed4Interval.h | 4 +
.../FileRecordTools/Records/Bed5Interval.cpp | 15 ++
.../FileRecordTools/Records/Bed5Interval.h | 4 +
.../FileRecordTools/Records/Bed6Interval.cpp | 17 ++
.../FileRecordTools/Records/Bed6Interval.h | 4 +
.../Records/BedGraphInterval.cpp | 12 +
.../Records/BedGraphInterval.h | 4 +
.../Records/BedPlusInterval.cpp | 29 +--
.../FileRecordTools/Records/BedPlusInterval.h | 4 +-
src/utils/FileRecordTools/Records/Record.cpp | 14 ++
src/utils/FileRecordTools/Records/Record.h | 3 +
16 files changed, 236 insertions(+), 123 deletions(-)
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
index cde07329..4c5cd8dc 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -1,3 +1,10 @@
+/*
+ * 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);
}
+
+
+
diff --git a/src/utils/FileRecordTools/Records/BamRecord.h b/src/utils/FileRecordTools/Records/BamRecord.h
index 262ef1ab..b74dbc2c 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.h
+++ b/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
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.cpp b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
index 742ea7b9..3f896be5 100644
--- a/src/utils/FileRecordTools/Records/Bed3Interval.cpp
+++ b/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;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.h b/src/utils/FileRecordTools/Records/Bed3Interval.h
index a3015e0b..9f1ff118 100644
--- a/src/utils/FileRecordTools/Records/Bed3Interval.h
+++ b/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();
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.cpp b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
index 13f5265e..c1ef81a3 100644
--- a/src/utils/FileRecordTools/Records/Bed4Interval.cpp
+++ b/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;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.h b/src/utils/FileRecordTools/Records/Bed4Interval.h
index 4d9fda7a..f42817c4 100644
--- a/src/utils/FileRecordTools/Records/Bed4Interval.h
+++ b/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();
};
diff --git a/src/utils/FileRecordTools/Records/Bed5Interval.cpp b/src/utils/FileRecordTools/Records/Bed5Interval.cpp
index 8e643608..7307fb66 100644
--- a/src/utils/FileRecordTools/Records/Bed5Interval.cpp
+++ b/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;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed5Interval.h b/src/utils/FileRecordTools/Records/Bed5Interval.h
index 01d65966..bc913d1d 100644
--- a/src/utils/FileRecordTools/Records/Bed5Interval.h
+++ b/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();
};
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.cpp b/src/utils/FileRecordTools/Records/Bed6Interval.cpp
index b486333a..8371553a 100644
--- a/src/utils/FileRecordTools/Records/Bed6Interval.cpp
+++ b/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;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.h b/src/utils/FileRecordTools/Records/Bed6Interval.h
index 91a00e09..9ad9f80b 100644
--- a/src/utils/FileRecordTools/Records/Bed6Interval.h
+++ b/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();
};
diff --git a/src/utils/FileRecordTools/Records/BedGraphInterval.cpp b/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
index e089782c..e0808573 100644
--- a/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
+++ b/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;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/BedGraphInterval.h b/src/utils/FileRecordTools/Records/BedGraphInterval.h
index f3d612e8..1bdf619a 100644
--- a/src/utils/FileRecordTools/Records/BedGraphInterval.h
+++ b/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();
};
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp b/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
index d3e0c01a..fc8be368 100644
--- a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
+++ b/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);
}
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.h b/src/utils/FileRecordTools/Records/BedPlusInterval.h
index 4ebd3b67..4b98b4f3 100644
--- a/src/utils/FileRecordTools/Records/BedPlusInterval.h
+++ b/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; }
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index 6bad45dd..8e7d7911 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/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);
+// }
+}
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 92df4bad..2c303d90 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/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).
--
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