From f12f568c80c3201b84fc16d23ef9b6cd1bd270c4 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 31 Aug 2011 11:48:07 -0400
Subject: [PATCH] Added -S to closestBed
---
src/closestBed/closestBed.cpp | 8 +++++---
src/closestBed/closestBed.h | 5 +++--
src/closestBed/closestMain.cpp | 23 ++++++++++++++++++-----
3 files changed, 26 insertions(+), 10 deletions(-)
diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
index 635bdf85..dcd44a1d 100644
--- a/src/closestBed/closestBed.cpp
+++ b/src/closestBed/closestBed.cpp
@@ -21,11 +21,13 @@ const int SLOPGROWTH = 2048000;
/*
Constructor
*/
-BedClosest::BedClosest(string &bedAFile, string &bedBFile, bool forceStrand, string &tieMode, bool reportDistance, bool ignoreOverlaps)
+BedClosest::BedClosest(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand,
+ string &tieMode, bool reportDistance, bool ignoreOverlaps)
: _bedAFile(bedAFile)
, _bedBFile(bedBFile)
, _tieMode(tieMode)
- , _forceStrand(forceStrand)
+ , _sameStrand(sameStrand)
+ , _diffStrand(diffStrand)
, _reportDistance(reportDistance)
, _ignoreOverlaps(ignoreOverlaps)
{
@@ -76,7 +78,7 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
// THE HEAVY LIFTING
// search for hits with the current slop added
- _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _forceStrand);
+ _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _sameStrand, _diffStrand);
vector<BED>::const_iterator h = hits.begin();
vector<BED>::const_iterator hitsEnd = hits.end();
diff --git a/src/closestBed/closestBed.h b/src/closestBed/closestBed.h
index e5083003..0ee74d25 100644
--- a/src/closestBed/closestBed.h
+++ b/src/closestBed/closestBed.h
@@ -28,7 +28,7 @@ public:
// constructor
BedClosest(string &bedAFile, string &bedBFile,
- bool forceStrand, string &tieMode,
+ bool sameStrand, bool diffStrand, string &tieMode,
bool reportDistance, bool ignoreOverlaps);
// destructor
@@ -43,7 +43,8 @@ private:
string _bedAFile;
string _bedBFile;
string _tieMode;
- bool _forceStrand;
+ bool _sameStrand;
+ bool _diffStrand;
bool _reportDistance;
bool _ignoreOverlaps;
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index d34e01ff..d2f4fce7 100644
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -36,7 +36,8 @@ int main(int argc, char* argv[]) {
bool haveBedA = false;
bool haveBedB = false;
bool haveTieMode = false;
- bool forceStrand = false;
+ bool sameStrand = false;
+ bool diffStrand = false;
bool ignoreOverlaps = false;
bool reportDistance = false;
@@ -75,7 +76,10 @@ int main(int argc, char* argv[]) {
}
}
else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
- forceStrand = true;
+ sameStrand = true;
+ }
+ else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
+ diffStrand = true;
}
else if (PARAMETER_CHECK("-d", 2, parameterLength)) {
reportDistance = true;
@@ -108,8 +112,13 @@ int main(int argc, char* argv[]) {
showHelp = true;
}
+ if (sameStrand && diffStrand) {
+ cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
+ showHelp = true;
+ }
+
if (!showHelp) {
- BedClosest *bc = new BedClosest(bedAFile, bedBFile, forceStrand, tieMode, reportDistance, ignoreOverlaps);
+ BedClosest *bc = new BedClosest(bedAFile, bedBFile, sameStrand, diffStrand, tieMode, reportDistance, ignoreOverlaps);
delete bc;
return 0;
}
@@ -131,8 +140,12 @@ void ShowHelp(void) {
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
cerr << "Options: " << endl;
- cerr << "\t-s\t" << "Force strandedness. That is, find the closest feature in B" << endl;
- cerr << "\t\tthat overlaps A on the same strand." << endl;
+ cerr << "\t-s\t" << "Require same strandedness. That is, find the closest feature in B" << endl;
+ cerr << "\t\tthat overlaps A on the _same_ strand." << endl;
+ cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-s\t" << "Require opposite strandedness. That is, find the closest feature in B" << endl;
+ cerr << "\t\tthat overlaps A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
cerr << "\t-d\t" << "In addition to the closest feature in B, " << endl;
--
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