Merge pull request #43 from nkindlon/master

Fixed intersect bug so that bed query with Bam DB correctly gives bed ou...

src/utils/Contexts/ContextBase.cpp

@@ -94,15 +94,9 @@ bool ContextBase::determineOutputType() {
 		return true;
 	}
 
-	//Otherwise, if there are any BAM files in the input,
-	//then the output should be BAM.
-	for (_i = 0; _i < (int)_files.size(); _i++) {
-		if (_files[_i]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
-			setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
-			_bamHeaderAndRefIdx = _i;
-			_outputTypeDetermined = true;
-			return true;
-		}
+	//Otherwise, if the input is BAM, then the output is BAM
+	if (getFile(0)->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+		setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
 	}
 
 	//Okay, it's bed.

test/intersect/test-intersect.sh

@@ -446,7 +446,16 @@ echo \
 "chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I11^I21^I345.7^Iwhy?^I+" > exp
 $BT intersect -a bed6.strand.bed -b bed6.strand2.bed -wa -wb -S | cat -t > obs
 check obs exp
-
 rm obs exp
 
+##################################################################
+#  Test that intersect of bed query with BAM DB gives Bed output.
+##################################################################
+echo "    intersect.t37...\c"
+echo \
+"chr1	10	20	a1	1	+
+chr1	100	200	a2	2	-" > exp
+$BT intersect -a a.bed -b a.bam > obs
+
+
 rm one_block.bam two_blocks.bam three_blocks.bam
\ No newline at end of file