Unmapped BAM alignments are now captured by -v in intersectBed and windowBed....

Unmapped BAM alignments are now captured by -v in intersectBed and windowBed. Thanks to Davide Cittaro.

src/intersectBed/intersectBed.cpp

@@ -278,6 +278,10 @@ void BedIntersect::IntersectBam(string bamFile) {
                 bool overlapsFound = false;
                 // treat the BAM alignment as a single "block"
                 if (_obeySplits == false) {
+                    // Toying with adding tags.  Need new version of FindOverlaps.
+                    // FindOverlaps(a, hits);
+                    // bam.AddTag("YB", "i", static_cast<int>(hits.size()));
+                    // hits.clear();
                     overlapsFound = FindOneOrMoreOverlap(a);
                 }
                 // split the BAM alignment into discrete blocks and
@@ -327,6 +331,10 @@ void BedIntersect::IntersectBam(string bamFile) {
                 }
             }
         }
+        // BAM IsMapped() is false
+        else if (_noHit == true) {
+            writer.SaveAlignment(bam);
+        }
     }
 
     // close the relevant BAM files.

src/windowBed/windowBed.cpp

@@ -204,6 +204,10 @@ void BedWindow::WindowIntersectBam(string bamFile) {
                 hits.clear();
             }
         }
+        // BAM IsMapped() is false
+        else if (_noHit == true) {
+            writer.SaveAlignment(bam);
+        }
     }
 
     // close the relevant BAM files.