Added -S to coverageBed

src/coverageBed/coverageBed.cpp

@@ -13,7 +13,7 @@
 #include "coverageBed.h"
 
 // build
-BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool forceStrand,
+BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand,
                          bool writeHistogram, bool bamInput, bool obeySplits, 
                          bool eachBase, bool countsOnly) {
 
@@ -23,7 +23,8 @@ BedCoverage::BedCoverage(string &bedAFile, string &bedBFile, bool forceStrand,
     _bedA           = new BedFile(bedAFile);
     _bedB           = new BedFile(bedBFile);
 
-    _forceStrand    = forceStrand;
+    _sameStrand     = sameStrand;
+    _diffStrand     = diffStrand;
     _obeySplits     = obeySplits;
     _eachBase       = eachBase;
     _writeHistogram = writeHistogram;
@@ -60,7 +61,7 @@ void BedCoverage::CollectCoverageBed() {
         if (bedStatus == BED_VALID) {
             // process the BED entry as a single block
             if (_obeySplits == false)
-                _bedB->countHits(a, _forceStrand, _countsOnly);
+                _bedB->countHits(a, _sameStrand, _diffStrand, _countsOnly);
             // split the BED into discrete blocksand process each independently.
             else {
                 bedVector bedBlocks;
@@ -68,7 +69,7 @@ void BedCoverage::CollectCoverageBed() {
 
                 // use countSplitHits to avoid over-counting each split chunk
                 // as distinct read coverage.
-                _bedB->countSplitHits(bedBlocks, _forceStrand, _countsOnly);
+                _bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly);
             }
             a = nullBed;
         }
@@ -112,7 +113,7 @@ void BedCoverage::CollectCoverageBam(string bamFile) {
                 a.strand = "+";
                 if (bam.IsReverseStrand()) a.strand = "-";
 
-                _bedB->countHits(a, _forceStrand, _countsOnly);
+                _bedB->countHits(a, _sameStrand, _diffStrand, _countsOnly);
             }
             // split the BAM alignment into discrete blocks and
             // look for overlaps only within each block.
@@ -124,7 +125,7 @@ void BedCoverage::CollectCoverageBam(string bamFile) {
                 getBamBlocks(bam, refs, bedBlocks, true);
                 // use countSplitHits to avoid over-counting each split chunk
                 // as distinct read coverage.
-                _bedB->countSplitHits(bedBlocks, _forceStrand, _countsOnly);
+                _bedB->countSplitHits(bedBlocks, _sameStrand, _diffStrand, _countsOnly);
             }
         }
     }

src/coverageBed/coverageBed.h

@@ -36,7 +36,7 @@ class BedCoverage {
 public:
 
     // constructor
-    BedCoverage(string &bedAFile, string &bedBFile, bool forceStrand, bool writeHistogram,
+    BedCoverage(string &bedAFile, string &bedBFile, bool sameStrand, bool diffStrand, bool writeHistogram,
                 bool bamInput, bool obeySplits, bool eachBase, bool countsOnly);
 
     // destructor
@@ -51,8 +51,9 @@ private:
     // instance of a bed file class.
     BedFile *_bedA, *_bedB;
 
-    // do we care about strandedness when counting coverage?
-    bool _forceStrand;
+    // do we care about same or opposite strandedness when counting coverage?
+    bool _sameStrand;
+    bool _diffStrand;
 
     // should we write a histogram for each feature in B?
     bool _writeHistogram;

src/coverageBed/coverageMain.cpp

@@ -33,7 +33,8 @@ int main(int argc, char* argv[]) {
     string bedBFile;
 
     // parm flags
-    bool forceStrand    = false;
+    bool sameStrand    = false;
+    bool diffStrand    = false;
     bool writeHistogram = false;
     bool eachBase       = false;
     bool obeySplits     = false;
@@ -84,7 +85,10 @@ 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("-hist", 5, parameterLength)) {
             writeHistogram = true;
@@ -109,9 +113,15 @@ int main(int argc, char* argv[]) {
         cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
         showHelp = true;
     }
+    
+    if (sameStrand && diffStrand) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
 
     if (!showHelp) {
-        BedCoverage *bg = new BedCoverage(bedAFile, bedBFile, forceStrand, writeHistogram, bamInput, obeySplits, eachBase, countsOnly);
+        BedCoverage *bg = new BedCoverage(bedAFile, bedBFile, sameStrand, diffStrand,
+                                          writeHistogram, bamInput, obeySplits, eachBase, countsOnly);
         delete bg;
         return 0;
     }
@@ -135,9 +145,13 @@ void ShowHelp(void) {
 
     cerr << "\t-abam\t"         << "The A input file is in BAM format." << endl << endl;
 
-    cerr << "\t-s\t"            << "Force strandedness.  That is, only include hits in A that" << endl;
-    cerr                        << "\t\toverlap B on the same strand." << endl;
-    cerr                        << "\t\t- By default, hits are included without respect to strand." << endl << endl;
+    cerr << "\t-s\t"            << "Require same strandedness.  That is, only counts hits in A that" << endl;
+    cerr                        << "\t\toverlap B on the _same_ strand." << endl;
+    cerr                        << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
+
+    cerr << "\t-S\t"            << "Require different strandedness.  That is, only report hits in A that" << endl;
+    cerr                        << "\t\toverlap B on the _opposite_ strand." << endl;
+    cerr                        << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
 
     cerr << "\t-hist\t"         << "Report a histogram of coverage for each feature in B" << endl;
     cerr                        << "\t\tas well as a summary histogram for _all_ features in B." << endl << endl;