From fdee9c46a4268c7aeb4087203e692e6ad392e6ea Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 19 Jan 2011 12:54:38 -0500
Subject: [PATCH] Issue #50. SlopBed now adds percent-based slop to features
with the -pct option.
---
src/slopBed/slopBed.cpp | 30 +++++++++++++++++++-----------
src/slopBed/slopBed.h | 11 ++++++-----
src/slopBed/slopBedMain.cpp | 32 ++++++++++++++++++++------------
3 files changed, 45 insertions(+), 28 deletions(-)
diff --git a/src/slopBed/slopBed.cpp b/src/slopBed/slopBed.cpp
index 0403200f..c4cd1151 100644
--- a/src/slopBed/slopBed.cpp
+++ b/src/slopBed/slopBed.cpp
@@ -7,24 +7,25 @@
University of Virginia
aaronquinlan@gmail.com
- Licenced under the GNU General Public License 2.0 license.
+ Licensed under the GNU General Public License 2.0 license.
******************************************************************************/
#include "lineFileUtilities.h"
#include "slopBed.h"
-BedSlop::BedSlop(string &bedFile, string &genomeFile, bool &forceStrand, int &leftSlop, int &rightSlop) {
+BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) {
_bedFile = bedFile;
_genomeFile = genomeFile;
_forceStrand = forceStrand;
-
- _leftSlop = leftSlop;
- _rightSlop = rightSlop;
+ _leftSlop = leftSlop;
+ _rightSlop = rightSlop;
+ _fractional = fractional;
_bed = new BedFile(bedFile);
_genome = new GenomeFile(genomeFile);
+ // get going, slop it up.
SlopBed();
}
@@ -44,7 +45,14 @@ void BedSlop::SlopBed() {
bedStatus = _bed->GetNextBed(bedEntry, lineNum);
while (bedStatus != BED_INVALID) {
if (bedStatus == BED_VALID) {
- AddSlop(bedEntry);
+ if (_fractional == false) {
+ AddSlop(bedEntry, _leftSlop, _rightSlop);
+ }
+ else {
+ int leftSlop = (int) (_leftSlop * bedEntry.size());
+ int rightSlop = (int) (_rightSlop * bedEntry.size());
+ AddSlop(bedEntry, leftSlop, rightSlop);
+ }
_bed->reportBedNewLine(bedEntry);
bedEntry = nullBed;
}
@@ -54,7 +62,7 @@ void BedSlop::SlopBed() {
}
-void BedSlop::AddSlop(BED &bed) {
+void BedSlop::AddSlop(BED &bed, int leftSlop, int rightSlop) {
// special handling if the BED entry is on the negative
// strand and the user cares about strandedness.
@@ -62,20 +70,20 @@ void BedSlop::AddSlop(BED &bed) {
if ( (_forceStrand) && (bed.strand == "-") ) {
// inspect the start
- if ( (static_cast<int>(bed.start) - _rightSlop) > 0 ) bed.start -= _rightSlop;
+ if ( (static_cast<int>(bed.start) - rightSlop) > 0 ) bed.start -= rightSlop;
else bed.start = 0;
// inspect the start
- if ( (static_cast<int>(bed.end) + _leftSlop) <= static_cast<int>(chromSize)) bed.end += _leftSlop;
+ if ( (static_cast<int>(bed.end) + leftSlop) <= static_cast<int>(chromSize)) bed.end += leftSlop;
else bed.end = chromSize;
}
else {
// inspect the start
- if ( (static_cast<int>(bed.start) - _leftSlop) > 0) bed.start -= _leftSlop;
+ if ( (static_cast<int>(bed.start) - leftSlop) > 0) bed.start -= leftSlop;
else bed.start = 0;
// inspect the end
- if ( (static_cast<int>(bed.end) + _rightSlop) <= static_cast<int>(chromSize)) bed.end += _rightSlop;
+ if ( (static_cast<int>(bed.end) + rightSlop) <= static_cast<int>(chromSize)) bed.end += rightSlop;
else bed.end = chromSize;
}
}
diff --git a/src/slopBed/slopBed.h b/src/slopBed/slopBed.h
index 48d36f4f..d22590c7 100644
--- a/src/slopBed/slopBed.h
+++ b/src/slopBed/slopBed.h
@@ -30,7 +30,7 @@ class BedSlop {
public:
// constructor
- BedSlop(string &bedFile, string &genomeFile, bool &forceStrand, int &leftSlop, int &rightSlop) ;
+ BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional);
// destructor
~BedSlop(void);
@@ -42,9 +42,10 @@ private:
string _bedFile;
string _genomeFile;
- bool _forceStrand;
- int _leftSlop;
- int _rightSlop;
+ bool _forceStrand;
+ float _leftSlop;
+ float _rightSlop;
+ bool _fractional;
BedFile *_bed;
GenomeFile *_genome;
@@ -54,5 +55,5 @@ private:
void SlopBed();
// method to add requested "slop" to a single BED entry
- void AddSlop(BED &bed);
+ void AddSlop(BED &bed, int leftSlop, int rightSlop);
};
diff --git a/src/slopBed/slopBedMain.cpp b/src/slopBed/slopBedMain.cpp
index 3e490de0..149cc377 100644
--- a/src/slopBed/slopBedMain.cpp
+++ b/src/slopBed/slopBedMain.cpp
@@ -40,8 +40,9 @@ int main(int argc, char* argv[]) {
bool haveBoth = false;
bool forceStrand = false;
- int leftSlop = 0;
- int rightSlop = 0;
+ float leftSlop = 0.0;
+ float rightSlop = 0.0;
+ bool fractional = false;
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -75,28 +76,31 @@ int main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-l", 2, parameterLength)) {
if ((i+1) < argc) {
haveLeft = true;
- leftSlop = atoi(argv[i + 1]);
+ leftSlop = atof(argv[i + 1]);
i++;
}
}
else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
if ((i+1) < argc) {
haveRight = true;
- rightSlop = atoi(argv[i + 1]);
+ rightSlop = atof(argv[i + 1]);
i++;
}
}
else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
if ((i+1) < argc) {
haveBoth = true;
- leftSlop = atoi(argv[i + 1]);
- rightSlop = atoi(argv[i + 1]);
+ leftSlop = atof(argv[i + 1]);
+ rightSlop = atof(argv[i + 1]);
i++;
}
}
else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
forceStrand = true;
}
+ else if(PARAMETER_CHECK("-pct", 4, parameterLength)) {
+ fractional = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -122,7 +126,7 @@ int main(int argc, char* argv[]) {
}
if (!showHelp) {
- BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop);
+ BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional);
delete bc;
return 0;
@@ -144,18 +148,22 @@ void ShowHelp(void) {
cerr << "Options: " << endl;
cerr << "\t-b\t" << "Increase the BED/GFF/VCF entry by -b base pairs in each direction." << endl;
- cerr << "\t\t- (Integer)" << endl;
+ cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
cerr << "\t-l\t" << "The number of base pairs to subtract from the start coordinate." << endl;
- cerr << "\t\t- (Integer)" << endl;
-
+ cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+
cerr << "\t-r\t" << "The number of base pairs to add to the end coordinate." << endl;
- cerr << "\t\t- (Integer)" << endl;
-
+ cerr << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+
cerr << "\t-s\t" << "Define -l and -r based on strand." << endl;
cerr << "\t\tE.g. if used, -l 500 for a negative-stranded feature, " << endl;
cerr << "\t\tit will add 500 bp downstream. Default = false." << endl << endl;
+ cerr << "\t-pct\t" << "Define -l and -r as a fraction of the feature's length." << endl;
+ cerr << "\t\tE.g. if used on a 1000bp feature, -l 0.50, " << endl;
+ cerr << "\t\twill add 500 bp \"upstream\". Default = false." << endl << endl;
+
cerr << "Notes: " << endl;
cerr << "\t(1) Starts will be set to 0 if options would force it below 0." << endl;
cerr << "\t(2) Ends will be set to the chromosome length if requested slop would" << endl;
--
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