X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamConverter.h;fp=BamConverter.h;h=d36f3d10c4d4e78ab4351f7482477fc77d318e07;hb=142c0168622638bb25f09796c3598fab28a1f94c;hp=4ea7d3e673e3942e4de7a678acb5be15faf03c11;hpb=f0aa264bd96a2e742cfe186767db69270b896899;p=rsem.git

diff --git a/BamConverter.h b/BamConverter.h
index 4ea7d3e..d36f3d1 100644
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -227,7 +227,8 @@ inline void BamConverter::writeCollapsedLines() {
 				memcpy(bam_aux_get(tmp_b, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
 				tmp_b->core.qual = getMAPQ(prb);
 			}
-			else tmp_b->core.qual = getMAPQ(1.0);
+			// otherwise, just use the MAPQ score of the orignal alignment
+
 			samwrite(out, tmp_b);
 			if (isPaired) {
 				if (p != NULL) memcpy(bam_aux_get(tmp_b2, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));