diff --git a/src/bedToBam/bedToBam.cpp b/src/bedToBam/bedToBam.cpp
index 41f5c021634771563ed694e209d5de2ceb0471b8..3c55809f42a9206a77ee963fb674eecd0a88cd4f 100755
--- a/src/bedToBam/bedToBam.cpp
+++ b/src/bedToBam/bedToBam.cpp
@@ -184,8 +184,7 @@ void DetermineBedInput(BedFile *bed, GenomeFile *genome, bool isBED12, int mapQu
void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual) {
- // open the BAM file for writing.
- BamWriter writer;
+ BamWriter *writer = new BamWriter();
// build a BAM header from the genomeFile
RefVector refs;
@@ -193,37 +192,29 @@ void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED1
map<string, int, std::less<string> > chromToId;
MakeBamHeader(genome->getGenomeFileName(), refs, bamHeader, chromToId);
- // add the reference headers to the BAM file
- writer.Open("stdout", bamHeader, refs);
-
-
- string bedLine;
- int lineNum = 0; // current input line number
- vector<string> bedFields; // vector for a BED entry
- bedFields.reserve(12);
-
- // process each entry in A
- while (getline(bedInput, bedLine)) {
-
- lineNum++;
- Tokenize(bedLine,bedFields);
-
- BED theBed;
- BamAlignment theBam;
- if (bed->parseLine(theBed, bedFields, lineNum)) {
- if (bed->bedType >= 4) {
- ConvertBedToBam(theBed, theBam, chromToId, isBED12, mapQual, lineNum);
- writer.SaveAlignment(theBam);
- }
- else {
- cerr << "Error: BED entry without name found at line: " << lineNum << ". Exiting!" << endl;
- exit (1);
- }
+ // open a BAM and add the reference headers to the BAM file
+ writer->Open("stdout", bamHeader, refs);
+ // open the BED file for reading.
+ bed->Open();
+
+ // process each BED entry and convert to BAM
+ BED bedEntry, nullBed;
+ int lineNum = 0;
+ while (bed->GetNextBed(bedEntry, lineNum)) {
+ BamAlignment bamEntry;
+ if (bed->bedType >= 4) {
+ ConvertBedToBam(bedEntry, bamEntry, chromToId, isBED12, mapQual, lineNum);
+ writer->SaveAlignment(bamEntry);
}
- // reset for the next input line
- bedFields.clear();
+ else {
+ cerr << "Error: BED entry without name found at line: " << lineNum << ". Exiting!" << endl;
+ exit (1);
+ }
+ bedEntry = nullBed;
}
- writer.Close();
+ // close up
+ bed->Close();
+ writer->Close();
}
@@ -254,6 +245,8 @@ void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int, std::le
bam.InsertSize = 0;
bam.MateRefID = -1;
+ bam.CigarData.clear();
+
if (isBED12 == false) {
CigarOp cOp;
cOp.Type = 'M';
diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
index f339eec573821560c26858287fdf981bdae76c4e..5a016867e2c63e0446936687ba3d6b8907ef2562 100755
--- a/src/closestBed/closestBed.cpp
+++ b/src/closestBed/closestBed.cpp
@@ -178,7 +178,7 @@ void BedClosest::FindClosestBed() {
// that we can easily compare "A" to it for overlaps
_bedB->loadBedFileIntoMap();
- BED a;
+ BED a, nullBed;
int lineNum = 0; // current input line number
vector<BED> hits; // vector of potential hits
hits.reserve(100);
@@ -188,6 +188,7 @@ void BedClosest::FindClosestBed() {
while (_bedA->GetNextBed(a, lineNum)) {
FindWindowOverlaps(a, hits);
hits.clear();
+ a = nullBed;
}
_bedA->Close();
}
diff --git a/src/coverageBed/coverageBed.cpp b/src/coverageBed/coverageBed.cpp
index 13f619394d34533b59a9001b242ec3e1ac477a42..176c4f945f0559c206b1b323cd94d268653b5018 100755
--- a/src/coverageBed/coverageBed.cpp
+++ b/src/coverageBed/coverageBed.cpp
@@ -56,11 +56,12 @@ void BedCoverage::CollectCoverageBed() {
_bedB->loadBedFileIntoMap();
int lineNum = 0; // current input line number
- BED a;
+ BED a, nullBed;
// process each entry in A
while (_bedA->GetNextBed(a, lineNum)) {
// count a as a hit with all the relevant features in B
_bedB->countHits(a, _forceStrand);
+ a = nullBed;
}
// report the coverage (summary or histogram) for BED B.
diff --git a/src/genomeCoverageBed/genomeCoverageBed.cpp b/src/genomeCoverageBed/genomeCoverageBed.cpp
index 1d845c807935cb24071a4febf256c06f7b267604..79ddfeb625f09cbe9ebd8371e951b7e2cc1babb5 100755
--- a/src/genomeCoverageBed/genomeCoverageBed.cpp
+++ b/src/genomeCoverageBed/genomeCoverageBed.cpp
@@ -58,7 +58,7 @@ void BedGenomeCoverage::CoverageBed() {
int currChromSize = 0;
int start, end;
- BED a;
+ BED a, nullBed;
int lineNum = 0; // current input line number
_bed->Open();
@@ -109,6 +109,7 @@ void BedGenomeCoverage::CoverageBed() {
}
prevChrom = currChrom;
prevChromSize = currChromSize;
+ a = nullBed;
}
_bed->Close();
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 15491a6fdd0a8f77d6efa14d59819b13ff9db1a7..3137038a78fdb246cc41f837ea4fa7b27320d222 100755
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -194,13 +194,14 @@ void BedIntersect::IntersectBed() {
int lineNum = 0;
vector<BED> hits;
hits.reserve(100);
- BED a;
+ BED a, nullBed;
// open the "A" file, process each BED entry and searh for overlaps.
_bedA->Open();
while (_bedA->GetNextBed(a, lineNum) == true) {
FindOverlaps(a, hits);
hits.clear();
+ a = nullBed;
}
_bedA->Close();
diff --git a/src/linksBed/linksBed.cpp b/src/linksBed/linksBed.cpp
index 25097157f19d6a69330ac278cefc63f9289f7737..3f03f999604eea28fb7d7dc358a8db1bce8ddcd2 100755
--- a/src/linksBed/linksBed.cpp
+++ b/src/linksBed/linksBed.cpp
@@ -102,12 +102,13 @@ void BedLinks::CreateLinks() {
cout << "<h3>BED Entries from: stdin </h3>" << endl;
int lineNum = 0;
- BED bedEntry;
+ BED bedEntry, nullBed;
_bed->Open();
while (_bed->GetNextBed(bedEntry, lineNum)) {
bedEntry.count = 0;
WriteURL(bedEntry, base);
+ bedEntry = nullBed;
}
_bed->Close();
diff --git a/src/shuffleBed/shuffleBed.cpp b/src/shuffleBed/shuffleBed.cpp
index faa62d1ecf0db9263f483c041d299efb7cfa4375..4ed5ae1a821899f27ff9ecba7a666cdb187f4b00 100755
--- a/src/shuffleBed/shuffleBed.cpp
+++ b/src/shuffleBed/shuffleBed.cpp
@@ -67,12 +67,13 @@ BedShuffle::~BedShuffle(void) {
void BedShuffle::Shuffle() {
int lineNum = 0;
- BED bedEntry; // used to store the current BED line from the BED file.
+ BED bedEntry, nullBed; // used to store the current BED line from the BED file.
_bed->Open();
while (_bed->GetNextBed(bedEntry, lineNum)) {
ChooseLocus(bedEntry);
_bed->reportBedNewLine(bedEntry);
+ bedEntry = nullBed;
}
_bed->Close();
}
diff --git a/src/slopBed/slopBed.cpp b/src/slopBed/slopBed.cpp
index 118eb758146e63f48d5f1e918d1309c24fda60e5..ddf2c4f6ef0afa626a7bef8b9e4f7827f4868ec5 100755
--- a/src/slopBed/slopBed.cpp
+++ b/src/slopBed/slopBed.cpp
@@ -37,12 +37,13 @@ BedSlop::~BedSlop(void) {
void BedSlop::SlopBed() {
int lineNum = 0;
- BED bedEntry; // used to store the current BED line from the BED file.
+ BED bedEntry, nullBed; // used to store the current BED line from the BED file.
_bed->Open();
while (_bed->GetNextBed(bedEntry, lineNum)) {
AddSlop(bedEntry);
- _bed->reportBedNewLine(bedEntry);
+ _bed->reportBedNewLine(bedEntry);
+ bedEntry = nullBed;
}
_bed->Close();
}
diff --git a/src/subtractBed/subtractBed.cpp b/src/subtractBed/subtractBed.cpp
index 0bc3f7f3ea8a8df5ac3b3db83e55456603326691..aa571a0626743c24710f03743278dae14766215d 100755
--- a/src/subtractBed/subtractBed.cpp
+++ b/src/subtractBed/subtractBed.cpp
@@ -154,7 +154,7 @@ void BedSubtract::SubtractBed() {
// that we can easily compare "A" to it for overlaps
_bedB->loadBedFileIntoMap();
- BED a;
+ BED a, nullBed;
int lineNum = 0; // current input line number
vector<BED> hits; // vector of potential hits
// reserve some space
@@ -165,6 +165,7 @@ void BedSubtract::SubtractBed() {
while (_bedA->GetNextBed(a, lineNum)) {
FindAndSubtractOverlaps(a, hits);
hits.clear();
+ a = nullBed;
}
_bedA->Close();
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index d0457bf307a350b52ab089fe9bb202ce4f3490b2..b8b4e521a1433bbd31a5eba7849d5394fe1eff66 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -658,7 +658,7 @@ bool BedFile::parseGffLine (BED &bed, const vector<string> &lineVector, int line
void BedFile::loadBedFileIntoMap() {
- BED bedEntry;
+ BED bedEntry, nullBed;
int lineNum = 0;
Open();
@@ -667,6 +667,8 @@ void BedFile::loadBedFileIntoMap() {
bedEntry.count = 0;
bedEntry.minOverlapStart = INT_MAX;
bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+
+ bedEntry = nullBed;
}
Close();
}
@@ -674,7 +676,7 @@ void BedFile::loadBedFileIntoMap() {
void BedFile::loadBedFileIntoMapNoBin() {
- BED bedEntry;
+ BED bedEntry, nullBed;
int lineNum = 0;
Open();
@@ -682,6 +684,8 @@ void BedFile::loadBedFileIntoMapNoBin() {
bedEntry.count = 0;
bedEntry.minOverlapStart = INT_MAX;
bedMapNoBin[bedEntry.chrom].push_back(bedEntry);
+
+ bedEntry = nullBed;
}
Close();
}