Make the bam parser more robust

liulab-dfci · Mar 24, 2022 · 277a93d · 277a93d
1 parent 5080641
commit 277a93d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/alignments.hpp b/alignments.hpp
@@ -383,14 +383,14 @@ class Alignments
 	bool IsTemplateAligned()
 	{
 		if ( ( b->core.flag & 0xd ) == 0xd ||
-			( b->core.flag & 0x5 ) == 0x4 ) 
+			( b->core.flag & 0x5 ) == 0x4 || b->core.tid < 0) 
 			return false ;
 		return true ;
 	}
 
 	bool IsAligned() 
 	{
-		if ( b->core.flag & 0x4 )
+		if ( b->core.flag & 0x4 || b->core.tid < 0)
 			return false ;
 		return true ;
 	}