From adf85fd4335a5265f1882eb7afbf3151c3c11d67 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 31 Aug 2011 12:10:56 -0400
Subject: [PATCH] Added -Sm to windowBed
---
src/windowBed/windowBed.cpp | 9 +++++----
src/windowBed/windowBed.h | 5 +++--
src/windowBed/windowMain.cpp | 20 ++++++++++++++++----
3 files changed, 24 insertions(+), 10 deletions(-)
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index 95a78134..513d91fe 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -18,7 +18,7 @@
*/
BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
bool anyHit, bool noHit, bool writeCount, bool strandWindows,
- bool matchOnStrand, bool bamInput, bool bamOutput, bool isUncompressedBam) {
+ bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam) {
_bedAFile = bedAFile;
_bedBFile = bedBFile;
@@ -30,7 +30,8 @@ BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSl
_noHit = noHit;
_writeCount = writeCount;
_strandWindows = strandWindows;
- _matchOnStrand = matchOnStrand;
+ _matchOnSameStrand = matchOnSameStrand;
+ _matchOnDiffStrand = matchOnDiffStrand;
_bamInput = bamInput;
_bamOutput = bamOutput;
_isUncompressedBam = isUncompressedBam;
@@ -70,7 +71,7 @@ void BedWindow::FindWindowOverlaps(const BED &a, vector<BED> &hits) {
Now report the hits (if any) based on the window around a.
*/
// get the hits in B for the A feature
- _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _matchOnStrand);
+ _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _matchOnSameStrand, _matchOnDiffStrand);
int numOverlaps = 0;
@@ -114,7 +115,7 @@ bool BedWindow::FindOneOrMoreWindowOverlaps(const BED &a) {
CHRPOS aFudgeEnd;
AddWindow(a, aFudgeStart, aFudgeEnd);
- bool overlapsFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _matchOnStrand);
+ bool overlapsFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _matchOnSameStrand, _matchOnDiffStrand);
return overlapsFound;
}
diff --git a/src/windowBed/windowBed.h b/src/windowBed/windowBed.h
index 2256468e..84f1b1b1 100644
--- a/src/windowBed/windowBed.h
+++ b/src/windowBed/windowBed.h
@@ -34,7 +34,7 @@ public:
// constructor
BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
bool anyHit, bool noHit, bool writeCount, bool strandWindows,
- bool matchOnStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
+ bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
// destructor
~BedWindow(void);
@@ -49,7 +49,8 @@ private:
int _rightSlop;
bool _noHit;
bool _strandWindows;
- bool _matchOnStrand;
+ bool _matchOnSameStrand;
+ bool _matchOnDiffStrand;
bool _bamInput;
bool _bamOutput;
bool _isUncompressedBam;
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index b15854f2..982109e4 100644
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -46,7 +46,8 @@ int main(int argc, char* argv[]) {
bool haveLeft = false;
bool haveRight = false;
bool strandWindows = false;
- bool matchOnStrand = false;
+ bool matchOnSameStrand = false;
+ bool matchOnDiffStrand = false;
bool inputIsBam = false;
bool outputIsBam = true;
bool uncompressedBam = false;
@@ -108,7 +109,10 @@ int main(int argc, char* argv[]) {
strandWindows = true;
}
else if (PARAMETER_CHECK("-sm", 3, parameterLength)) {
- matchOnStrand = true;
+ matchOnSameStrand = true;
+ }
+ else if (PARAMETER_CHECK("-sm", 3, parameterLength)) {
+ matchOnDiffStrand = true;
}
else if (PARAMETER_CHECK("-w", 2, parameterLength)) {
if ((i+1) < argc) {
@@ -177,9 +181,14 @@ int main(int argc, char* argv[]) {
showHelp = true;
}
+ if (matchOnSameStrand && matchOnDiffStrand) {
+ cerr << endl << "*****" << endl << "*****ERROR: Use either -sm or -Sm, not both." << endl << "*****" << endl;
+ showHelp = true;
+ }
+
if (!showHelp) {
BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit,
- noHit, writeCount, strandWindows, matchOnStrand,
+ noHit, writeCount, strandWindows, matchOnSameStrand, matchOnDiffStrand,
inputIsBam, outputIsBam, uncompressedBam);
delete bi;
return 0;
@@ -233,7 +242,10 @@ void ShowHelp(void) {
cerr << "\t\tfor a negative-stranded feature will add 500 bp downstream." << endl;
cerr << "\t\t- Default = disabled." << endl << endl;
- cerr << "\t-sm\t" << "Only report hits in B that overlap A on the same strand." << endl;
+ cerr << "\t-sm\t" << "Only report hits in B that overlap A on the _same_ strand." << endl;
+ cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-Sm\t" << "Only report hits in B that overlap A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
--
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