X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=BamWriter.h;h=e29e36bef54f6b6e8d40d30746204fb3f78eea8e;hp=b39400f5cb9d21c50d2dcdf8ac0222218c5f2286;hb=1c7a81621434a852a7f7e11d61621e50ba1b7f2a;hpb=86e650e9577999a7ba00ab454d1f6bf674b0ea70

diff --git a/BamWriter.h b/BamWriter.h
index b39400f..e29e36b 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -263,7 +263,7 @@ void BamWriter::work(HitWrapper<SingleHit> wrapper, Transcripts& transcripts) {
 					*p = 'Z'; ++p; *p = 'W'; ++p; *p = 'f'; ++p;
 					float val = (float)hmapIter->second;
 					memcpy(p, &val, 4);
-					samwrite(out, tmp_b);
+					if (tmp_b->core.qual > 0) samwrite(out, tmp_b); // output only when MAPQ > 0
 					bam_destroy1(tmp_b); // now hmapIter->b makes no sense
 				}
 				hmap.clear();
@@ -290,7 +290,7 @@ void BamWriter::work(HitWrapper<SingleHit> wrapper, Transcripts& transcripts) {
 			*p = 'Z'; ++p; *p = 'W'; ++p; *p = 'f'; ++p;
 			float val = (float)hmapIter->second;
 			memcpy(p, &val, 4);
-			samwrite(out, tmp_b);
+			if (tmp_b->core.qual > 0) samwrite(out, tmp_b); // If MAPQ is equal to 0, do not output this alignment
 			bam_destroy1(tmp_b); // now hmapIter->b makes no sense
 		}
 		hmap.clear();
@@ -429,9 +429,12 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper, Transcripts& transcripts)
 					float val = (float)hmapIter->second;
 					memcpy(p, &val, 4);
 					memcpy(p2, &val, 4);
-
-					samwrite(out, tmp_b);
-					samwrite(out, tmp_b2);
+					
+					// If MAPQ is equal to 0, do not output this alignment pair
+					if (tmp_b->core.qual > 0) {
+					  samwrite(out, tmp_b);
+					  samwrite(out, tmp_b2);
+					}
 
 					bam_destroy1(tmp_b);
 					bam_destroy1(tmp_b2);
@@ -467,8 +470,10 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper, Transcripts& transcripts)
 			memcpy(p, &val, 4);
 			memcpy(p2, &val, 4);
 
-			samwrite(out, tmp_b);
-			samwrite(out, tmp_b2);
+			if (tmp_b->core.qual > 0) {
+			  samwrite(out, tmp_b);
+			  samwrite(out, tmp_b2);
+			}
 
 			bam_destroy1(tmp_b);
 			bam_destroy1(tmp_b2);