X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamWriter.h;h=f664710245ff265e184f922c642c0d3efc74a29a;hb=c678676b7da64266b4b98258a34d1b32372da6dd;hp=782f5bdeb6705748a8919265e854b54d1f418133;hpb=509ffe2d71cf6a6f5cca8c39909f8ee10b8db899;p=rsem.git

diff --git a/BamWriter.h b/BamWriter.h
index 782f5bd..f664710 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -144,6 +144,8 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 		  b->core.mpos = b2->core.pos;
 		  b2->core.mpos = b->core.pos;
 		}
+
+		/*
 		else {
 		  // if only one mate can be aligned, mask it as unaligned and put an additional tag Z0:A:!
 		  char exclamation = '!';
@@ -156,7 +158,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 		    bam_aux_append(b2, "Z0", 'A', bam_aux_type2size('A'), (uint8_t*)&exclamation);
 		  }
 		}
-
+		*/
 
 		samwrite(out, b);
 		samwrite(out, b2);