Merge pull request #14 from nkindlon/master

Added fix for Bam files with empty headers. Added test for this to unit ...

src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp

@@ -204,10 +204,7 @@ bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar)
 
 
 			_bamReader = new BamTools::BamReader();
-			_bamReader->OpenStream(_finalInputStream);
-			QuickString bamHeader(_bamReader->GetHeaderText());
-
-			if (bamHeader.empty()) {
+			if (!_bamReader->OpenStream(_finalInputStream)) {
 				//This is NOT a bam file, but it is bgzipped.
 				_pushBackStreamBuf->clear();
 				//Put all bytes read so far back onto the scan buffer, then reset

test/intersect/gdc_exp

+chr2L	10	15	None	255	+	10	15	0,0,0	1	5,	0,
+chr2L	70	75	None	255	-	70	75	0,0,0	1	5,	0,
+chr2L	70	75	None	255	-	70	75	0,0,0	1	5,	0,
+chr2L	140	145	None	255	-	140	145	0,0,0	1	5,	0,
+chr2L	140	145	None	255	-	140	145	0,0,0	1	5,	0,
+chr2L	150	155	None	255	-	150	155	0,0,0	1	5,	0,
+chr2L	210	215	None	255	+	210	215	0,0,0	1	5,	0,
+chr2L	70	75	None	255	+	70	75	0,0,0	1	5,	0,
+chr2L	70	75	None	255	+	70	75	0,0,0	1	5,	0,
+chr2L	140	145	None	255	+	140	145	0,0,0	1	5,	0,
+chr2L	140	145	None	255	+	140	145	0,0,0	1	5,	0,
+chr2L	160	165	None	255	+	160	165	0,0,0	1	5,	0,

test/intersect/new_test-intersect.sh

@@ -605,6 +605,15 @@ check obs exp
 rm obs exp
 
 
+###########################################################
+#  Test that we can process a Bam file with no text in 
+#  it's header. 
+############################################################
+echo "    intersect.new.t53...\c"
+$BT intersect -a gdc.bam -b gdc.bam -bed > obs
+check obs gdc_exp
+rm obs
+