handle unaligned BAMs with -v

src/intersectBed/intersectBed.cpp

@@ -323,12 +323,12 @@ void BedIntersect::IntersectBam(string bamFile) {
     // get each set of alignments for each pair.
     while (reader.GetNextAlignment(bam)) {
 
-        // BAM IsMapped() is false
-        if ((!bam.IsMapped()) && (_noHit == true))
-            writer.SaveAlignment(bam);
-        else if (!bam.IsMapped())
+        // save an unaligned read if -v
+        if (!bam.IsMapped()) {
+            if (_noHit == true)
+                writer.SaveAlignment(bam);
             continue;
-
+        }   
         // break alignment into discrete blocks,
         bedVector bed_blocks;
         string chrom = refs.at(bam.RefID).RefName;

test/intersect/mapped_and_unmapped.sam

+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chr1	LN:249250621
+mapped	16	chr1	1	40	30M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50
+umapped	4	*	1	40	30M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50

test/intersect/test-intersect.sh

@@ -254,4 +254,25 @@ check obs exp
 rm obs exp
 
 
+
+##################################################################
+#  Test that only the mapped read is is found as an intersection
+##################################################################
+echo "    intersect.t23...\c"
+echo \
+"mapped	16	chr1	1	40	30M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50" > exp
+samtools view -Sb mapped_and_unmapped.sam 2>/dev/null | $BT intersect -abam - -b a.bed | samtools view - > obs 
+check obs exp
+rm obs exp
+
+##################################################################
+#  Test that an unmapped read is handled properly with -v
+##################################################################
+echo "    intersect.t24...\c"
+echo \
+"umapped	4	*	1	40	30M	*	0	0	GAAGGCCACCGCCGCGGTTATTTTCCTTCA	CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI	MD:Z:50" > exp
+samtools view -Sb mapped_and_unmapped.sam 2>/dev/null | $BT intersect -abam - -b a.bed -v | samtools view - > obs 
+check obs exp
+rm obs exp
+
 rm *.bam
\ No newline at end of file