removed redundant code that sets the secondary alignment flag for a r…

…eadpair
samtools · Jul 28, 2023 · 5404ca2 · 5404ca2
1 parent 6d3fc7b
commit 5404ca2
Showing 1 changed file with 0 additions and 7 deletions.
diff --git a/src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java b/src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
@@ -455,13 +455,6 @@ public List<SAMRecord> addPair(final String name, final int contig1, final int c
             end2.setSecondaryAlignment(true);
         }
 
-        if (record1NonPrimary) {
-            end1.setSecondaryAlignment(true);
-        }
-        if (record2NonPrimary) {
-            end2.setSecondaryAlignment(true);
-        }
-
         // set mate info
         SamPairUtil.setMateInfo(end1, end2, true);