For genome BAM, modified MD tag accordingly

[rsem.git] / SamParser.h

diff --git a/SamParser.h b/SamParser.h
index 513536f2a2107e181a0393946a00e9fa77c35416..e91f9c379539fc7ada0f8682bcfc7c957489d67f 100644 (file)
--- a/SamParser.h
+++ b/SamParser.h
@@ -341,10 +341,17 @@ inline int SamParser::getReadType(const bam1_t* b) {
        return (bam_aux2i(p) > 0 ? 2 : 0);
 }
 
-
 //For paired-end reads, do not print out type 2 reads
 inline int SamParser::getReadType(const bam1_t* b, const bam1_t* b2) {
-       if ((b->core.flag & 0x0002) && (b2->core.flag & 0x0002)) return 1;
+       if (!(b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) return 1;
+
+       if (!strcmp(rtTag, "")) return 0;
+
+       uint8_t *p = bam_aux_get(b, rtTag);
+       if (p != NULL && bam_aux2i(p) > 0) return 2;
+
+       p = bam_aux_get(b2, rtTag);
+       if (p != NULL && bam_aux2i(p) > 0) return 2;
 
        return 0;
 }