Added -f to tagBam.

src/tagBam/tagBam.cpp

@@ -14,12 +14,13 @@
 
 // build
 TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
-            const vector<string> &annoLables, bool forceStrand) :
+            const vector<string> &annoLables, bool forceStrand, float overlapFraction) :
 
     _bamFile(bamFile),
     _annoFileNames(annoFileNames),
     _annoLabels(annoLables),
-    _forceStrand(forceStrand)
+    _forceStrand(forceStrand),
+    _overlapFraction(overlapFraction)
 {}
 
 
@@ -49,7 +50,7 @@ void TagBam::CloseAnnoFiles() {
 
 bool TagBam::FindOneOrMoreOverlap(const BED &a, BedFile *bedFile) {
     return bedFile->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand,
-                                                _forceStrand, 0);
+                                                _forceStrand, _overlapFraction);
 }
 
 void TagBam::Tag() {

src/tagBam/tagBam.h

@@ -40,7 +40,7 @@ public:
 
     // constructor
     TagBam(const string &bamFile, const vector<string> &annoFileNames,
-                const vector<string> &annoLabels, bool forceStrand);
+                const vector<string> &annoLabels, bool forceStrand, float overlapFraction);
 
     // destructor
     ~TagBam(void);
@@ -61,6 +61,7 @@ private:
 
     // do we care about strandedness when tagging?
     bool _forceStrand;
+    float _overlapFraction;
 
     // private function for reporting coverage information
     void ReportAnnotations();

src/tagBam/tagBamMain.cpp

@@ -30,8 +30,10 @@ int main(int argc, char* argv[]) {
 
     // input file
     string bamFile;
+    float overlapFraction = 1E-9;
 
     // parm flags
+    bool haveFraction       = false;
     bool forceStrand    = false;
     bool haveBam        = false;
     bool haveFiles      = false;
@@ -98,6 +100,13 @@ int main(int argc, char* argv[]) {
         else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
             forceStrand = true;
         }
+        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveFraction = true;
+                overlapFraction = atof(argv[i + 1]);
+                i++;
+            }
+        }
         else {
             cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
             showHelp = true;
@@ -111,7 +120,7 @@ int main(int argc, char* argv[]) {
     }
 
     if (!showHelp) {
-        TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, forceStrand);
+        TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, forceStrand, overlapFraction);
         ba->Tag();
         delete ba;
         return 0;
@@ -137,5 +146,8 @@ void ShowHelp(void) {
     cerr << "\t-s\t"            << "Force strandedness.  That is, only tag alignments that have the same" << endl;
     cerr                        << "\t\tstrand as a feature in the annotation file(s)." << endl << endl;
 
+    cerr << "\t-f\t"            << "Minimum overlap required as a fraction of the alignment." << endl;
+    cerr                        << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
+    cerr                        << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
     exit(1);
 }