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fix memory leak in shiftBed #1094

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fix memory leak in shiftBed #1094

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40 changes: 18 additions & 22 deletions src/shiftBed/shiftBed.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -10,46 +10,42 @@
#include "lineFileUtilities.h"
#include "shiftBed.h"

BedShift::BedShift(string &bedFile, string &genomeFile, float shiftMinus,
float shiftPlus, bool fractional, bool printHeader) {

_bedFile = bedFile;
_genomeFile = genomeFile;
_shiftMinus = shiftMinus;
_shiftPlus = shiftPlus;
_fractional = fractional;
_printHeader = printHeader;

_bed = new BedFile(bedFile);
_genome = new GenomeFile(genomeFile);

BedShift::BedShift(const string &bedFile, const string &genomeFile, float shiftMinus,
float shiftPlus, bool fractional, bool printHeader) :
_bedFile(bedFile),
_genomeFile(genomeFile),
_shiftMinus(shiftMinus),
_shiftPlus(shiftPlus),
_fractional(fractional),
_printHeader(printHeader),
_bed(_bedFile),
_genome(genomeFile)
{
// get going, shift it around.
ShiftBed();
}

BedShift::~BedShift(void) {}

void BedShift::ShiftBed() {

BED bedEntry; // used to store the current BED line from the BED file.

_bed->Open();
_bed.Open();
// report header first if asked.
if (_printHeader == true) {
_bed->PrintHeader();
_bed.PrintHeader();
}
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
while (_bed.GetNextBed(bedEntry)) {
if (_bed._status == BED_VALID) {
AddShift(bedEntry);
_bed->reportBedNewLine(bedEntry);
_bed.reportBedNewLine(bedEntry);
}
}
_bed->Close();
_bed.Close();
}

void BedShift::AddShift(BED &bed) {

CHRPOS chromSize = (CHRPOS)_genome->getChromSize(bed.chrom);
CHRPOS chromSize = _genome.getChromSize(bed.chrom);

double shift;

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12 changes: 3 additions & 9 deletions src/shiftBed/shiftBed.h
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Original file line number Diff line number Diff line change
Expand Up @@ -28,12 +28,7 @@ class BedShift {
public:

// constructor
BedShift(string &bedFile, string &genomeFile, float shiftMinus, float shiftPlus, bool fractional, bool printHeader);

// destructor
~BedShift(void);


BedShift(const string &bedFile, const string &genomeFile, float shiftMinus, float shiftPlus, bool fractional, bool printHeader);

private:

Expand All @@ -45,11 +40,10 @@ class BedShift {
bool _fractional;
bool _printHeader;

BedFile *_bed;
GenomeFile *_genome;
BedFile _bed;
GenomeFile _genome;

// methods

void ShiftBed();

// method to add requested "slop" to a single BED entry
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