diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index 5bfbe87e98b4f0976bcb6e5c9246d230345be2a1..5640791d0f78bfd613f400e348a12ed1c2be0e24 100644
--- a/src/pairToBed/pairToBed.cpp
+++ b/src/pairToBed/pairToBed.cpp
@@ -33,13 +33,14 @@ bool IsCorrectMappingForBEDPE (const BamAlignment &bam) {
*/
BedIntersectPE::BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
- string searchType, bool forceStrand, bool bamInput,
+ string searchType, bool sameStrand, bool diffStrand, bool bamInput,
bool bamOutput, bool uncompressedBam, bool useEditDistance) {
_bedAFilePE = bedAFilePE;
_bedBFile = bedBFile;
_overlapFraction = overlapFraction;
- _forceStrand = forceStrand;
+ _sameStrand = sameStrand;
+ _diffStrand = diffStrand;
_useEditDistance = useEditDistance;
_searchType = searchType;
_bamInput = bamInput;
@@ -80,7 +81,7 @@ void BedIntersectPE::FindOverlaps(const BEDPE &a, vector<BED> &hits1, vector<BED
// make sure we have a valid chromosome before we search
if (a.chrom1 != ".") {
// Find the quality hits between ***end1*** of the BEDPE and the B BED file
- _bedB->FindOverlapsPerBin(a.chrom1, a.start1, a.end1, a.strand1, hits1, _forceStrand);
+ _bedB->FindOverlapsPerBin(a.chrom1, a.start1, a.end1, a.strand1, hits1, _sameStrand, _diffStrand);
vector<BED>::const_iterator h = hits1.begin();
vector<BED>::const_iterator hitsEnd = hits1.end();
@@ -110,7 +111,7 @@ void BedIntersectPE::FindOverlaps(const BEDPE &a, vector<BED> &hits1, vector<BED
// make sure we have a valid chromosome before we search
if (a.chrom2 != ".") {
// Now find the quality hits between ***end2*** of the BEDPE and the B BED file
- _bedB->FindOverlapsPerBin(a.chrom2, a.start2, a.end2, a.strand2, hits2, _forceStrand);
+ _bedB->FindOverlapsPerBin(a.chrom2, a.start2, a.end2, a.strand2, hits2, _sameStrand, _diffStrand);
vector<BED>::const_iterator h = hits2.begin();
vector<BED>::const_iterator hitsEnd = hits2.end();
@@ -198,7 +199,7 @@ bool BedIntersectPE::FindOneOrMoreOverlaps(const BEDPE &a, const string &type) {
// Look for overlaps in end 1 assuming we have an aligned chromosome.
if (a.chrom1 != ".") {
end1Found = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom1, a.start1, a.end1, a.strand1,
- _forceStrand, _overlapFraction);
+ _sameStrand, _diffStrand, _overlapFraction);
// can we bail out without checking end2?
if ((type == "either") && (end1Found == true)) return true;
@@ -210,7 +211,7 @@ bool BedIntersectPE::FindOneOrMoreOverlaps(const BEDPE &a, const string &type) {
// Now look for overlaps in end 2 assuming we have an aligned chromosome.
if (a.chrom2 != ".") {
end2Found = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom2, a.start2, a.end2, a.strand2,
- _forceStrand, _overlapFraction);
+ _sameStrand, _diffStrand, _overlapFraction);
if ((type == "either") && (end2Found == true)) return true;
else if ((type == "neither") && (end2Found == true)) return false;
@@ -271,7 +272,7 @@ void BedIntersectPE::FindSpanningOverlaps(const BEDPE &a, vector<BED> &hits, con
spanLength = spanEnd - spanStart;
// get the hits for the span
- _bedB->FindOverlapsPerBin(a.chrom1, spanStart, spanEnd, a.strand1, hits, _forceStrand);
+ _bedB->FindOverlapsPerBin(a.chrom1, spanStart, spanEnd, a.strand1, hits, _sameStrand, _diffStrand);
vector<BED>::const_iterator h = hits.begin();
vector<BED>::const_iterator hitsEnd = hits.end();
@@ -324,7 +325,7 @@ bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE &a, const string
spanLength = spanEnd - spanStart;
overlapFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom1, spanStart, spanEnd, a.strand1,
- _forceStrand, _overlapFraction);
+ _sameStrand, _diffStrand, _overlapFraction);
return overlapFound;
}
diff --git a/src/pairToBed/pairToBed.h b/src/pairToBed/pairToBed.h
index b85497ca77989903b83605449fc50570d84f6bf8..d881c565fb945f89fd8c51a99978c8cac611fe51 100644
--- a/src/pairToBed/pairToBed.h
+++ b/src/pairToBed/pairToBed.h
@@ -43,7 +43,7 @@ public:
// constructor
BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
- string searchType, bool forceStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance);
+ string searchType, bool sameStrand, bool diffStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance);
// destructor
~BedIntersectPE(void);
@@ -66,7 +66,8 @@ private:
string _bedBFile;
float _overlapFraction;
string _searchType;
- bool _forceStrand;
+ bool _sameStrand;
+ bool _diffStrand;
bool _useEditDistance;
bool _bamInput;
bool _bamOutput;
diff --git a/src/pairToBed/pairToBedMain.cpp b/src/pairToBed/pairToBedMain.cpp
index 068e6e3db1755a811f303edd844e2755693ec5c0..f29cf978d1fd0bbc08c628f68db0c672f3f42f52 100644
--- a/src/pairToBed/pairToBedMain.cpp
+++ b/src/pairToBed/pairToBedMain.cpp
@@ -41,7 +41,8 @@ int main(int argc, char* argv[]) {
bool haveBedB = false;
bool haveSearchType = false;
bool haveFraction = false;
- bool forceStrand = false;
+ bool sameStrand = false;
+ bool diffStrand = false;
bool useEditDistance = false;
bool inputIsBam = false;
bool outputIsBam = true;
@@ -110,7 +111,10 @@ 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("-ubam", 5, parameterLength)) {
uncompressedBam = true;
@@ -136,7 +140,7 @@ int main(int argc, char* argv[]) {
}
if ( ((searchType == "ispan") || (searchType == "ospan") || (searchType == "notispan") || (searchType == "notospan"))
- && forceStrand ) {
+ && (sameStrand || diffStrand) ) {
cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl;
showHelp = true;
}
@@ -145,11 +149,16 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl;
showHelp = true;
}
+
+ if (sameStrand && diffStrand) {
+ cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
+ showHelp = true;
+ }
if (!showHelp) {
BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction,
- searchType, forceStrand, inputIsBam,
+ searchType, sameStrand, diffStrand, inputIsBam,
outputIsBam, uncompressedBam, useEditDistance);
delete bi;
return 0;
@@ -190,7 +199,11 @@ void ShowHelp(void) {
cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
- cerr << "\t-s\t" << "Enforce strandedness when finding overlaps." << endl;
+ cerr << "\t-s\t" << "Require same strandedness when finding overlaps." << endl;
+ cerr << "\t\tDefault is to ignore stand." << endl;
+ cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;
+
+ cerr << "\t-S\t" << "Require different strandedness when finding overlaps." << endl;
cerr << "\t\tDefault is to ignore stand." << endl;
cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl;