Fixed bug where name conventions weren't tested for unsorted data; stopped...

Fixed bug where name conventions weren't tested for unsorted data; stopped namecheck on unmapped bam records

src/intersectFile/intersectFile.cpp

@@ -98,6 +98,7 @@ bool IntersectFile::nextUnsortedFind(RecordKeyVector &hits)
 		if (queryRecord == NULL) {
 			continue;
 		} else {
+			_context->testNameConventions(queryRecord);
 			hits.setKey(queryRecord);
 			 _binTree->getHits(queryRecord, hits);
 			return true;

src/utils/Contexts/ContextBase.cpp

@@ -650,7 +650,9 @@ bool ContextBase::parseIoBufSize(QuickString bufStr)
 }
 
 void ContextBase::testNameConventions(const Record *record) {
-	if (getNameCheckDisabled() || _nameConventionWarningTripped) return;
+	//Do nothing if using the -nonamecheck option,
+	//warning already given, or record is unmapped BAM record
+	if (getNameCheckDisabled() || _nameConventionWarningTripped || record->isUnmapped()) return;
 
 	int fileIdx = record->getFileIdx();
 

test/intersect/test-intersect.sh

@@ -537,16 +537,15 @@ check exp obs
 rm exp obs
 
 ##################################################################
-# see that -nonamecheck only works for sorted data
-# NOTE: This test is now deprecated, as the -nonamecheck option
-# must also now work with unsorted data
+# see that naming conventions are tested with unsorted data.
 ##################################################################
 echo "    intersect.t44...\c"
-echo ok
-#"***** ERROR: -nonamecheck option is only valid for sorted input. *****" > exp
-#$BT intersect -a nonamecheck_a.bed -b nonamecheck_b.bed -nonamecheck 2>&1 > /dev/null | cat - | head -2 | tail -1 > obs
-#check exp obs
-#rm exp obs
+echo \
+"***** WARNING: File nonamecheck_a.bed has a record where naming convention (leading zero) is inconsistent with other files:
+chr1	10	20" > exp
+$BT intersect -a nonamecheck_a.bed -b nonamecheck_b.bed 2>&1 > /dev/null | cat - | head -2 > obs
+check exp obs
+rm exp obs
 
 
 ##################################################################