Set mapq on supplemental alignments in SamPairUtil (#1737)

samtools · Feb 21, 2025 · 4cc0100 · 4cc0100
1 parent b868bf4
commit 4cc0100
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/src/main/java/htsjdk/samtools/SamPairUtil.java b/src/main/java/htsjdk/samtools/SamPairUtil.java
@@ -332,6 +332,7 @@ public static void setMateInformationOnSupplementalAlignment( final SAMRecord su
         else {
             supplemental.setAttribute(SAMTag.MC, null);
         }
+        supplemental.setAttribute(SAMTag.MQ, matePrimary.getMappingQuality());
     }
 
     /**