Fix an about reinitalizing an varible

alignments.hpp

@@ -123,6 +123,7 @@ class Alignments
 			if ( bam_cigar2qlen( &b->core, rawCigar ) != b->core.l_qseq ) 
 				continue ;
 
+			len = 0 ;
 			for ( i = 0 ; i < b->core.n_cigar ; ++i )
 			{
 				int op = rawCigar[i] & BAM_CIGAR_MASK ;
@@ -157,10 +158,12 @@ class Alignments
 				segments[ segCnt ].b = start + len - 1 ;
 				++segCnt ;
 			}
-
-			/*for ( i = 0 ; i < segCnt ; ++i )
-			  printf( "(%d %d) ", segments[i].a, segments[i].b ) ;
-			  printf( "\n" ) ;*/
+			/*if ( !strcmp( bam1_qname( b ), "chr1:109656301-109749401W:ENST00000490758.2:381:1480:1090:1290:X" ) )
+			{
+				for ( i = 0 ; i < segCnt ; ++i )
+					printf( "(%d %d) ", segments[i].a, segments[i].b ) ;
+				printf( "\n" ) ;
+			}*/
 
 			// Check whether the mates are compatible
 			//int mChrId = b->core.mtid ;
@@ -232,6 +235,11 @@ class Alignments
 		return 1 ;
 	}
 
+	int GetReadLength()
+	{
+		return b->core.l_qseq ;
+	}
+
 	bool IsReverse()
 	{
 		if ( b->core.flag & 0x10 )