Fix for issue #145. -f was incorrectly set to 0.0 when using -labels, -intervals, or -names.

src/tagBam/tagBam.cpp

@@ -110,7 +110,7 @@ void TagBam::Tag() {
                 // use the score field
                 else if (!_useNames && _useScores && !_useIntervals) {
                     anno->allHits(a.chrom, a.start, a.end, a.strand, 
-                                  hits, _sameStrand, _diffStrand, 0.0, false);
+                                  hits, _sameStrand, _diffStrand, _overlapFraction, false);
                     for (size_t i = 0; i < hits.size(); ++i) {
                         annotations << hits[i].score;
                         if (i < hits.size() - 1) annotations << ",";
@@ -121,7 +121,7 @@ void TagBam::Tag() {
                 // use the name field from the annotation files to populate tag
                 else if (_useNames && !_useScores && !_useIntervals) {
                     anno->allHits(a.chrom, a.start, a.end, a.strand, 
-                                  hits, _sameStrand, _diffStrand, 0.0, false);
+                                  hits, _sameStrand, _diffStrand, _overlapFraction, false);
                     for (size_t j = 0; j < hits.size(); ++j) {
                         annotations << hits[j].name;
                         if (j < hits.size() - 1) annotations << ",";
@@ -132,7 +132,7 @@ void TagBam::Tag() {
                 // use the full interval information annotation files to populate tag
                 else if (!_useNames && !_useScores && _useIntervals) {
                     anno->allHits(a.chrom, a.start, a.end, a.strand, 
-                                  hits, _sameStrand, _diffStrand,  0.0, false);
+                                  hits, _sameStrand, _diffStrand,  _overlapFraction, false);
                     for (size_t j = 0; j < hits.size(); ++j) {
                         annotations << _annoLabels[i]  << ":" << 
                                         hits[j].chrom  << ":" <<

src/tagBam/tagBamMain.cpp

@@ -176,6 +176,10 @@ int tagbam_main(int argc, char* argv[]) {
         cerr << endl << "*****" << endl << "*****ERROR: Custom tags should be at most two characters per the SAM specification. " << endl << "*****" << endl;
         showHelp = true;
     }
+    if (haveFraction && overlapFraction == 0.0) {
+        cerr << endl << "*****" << endl << "*****ERROR: -f must be > 0.0" << endl << "*****" << endl;
+        showHelp = true;
+    }
 
 
     if (!showHelp) {