Added -Sm to windowBed

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;
 }
 

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;

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;