From 5404ca2759f3bcdb640561ff7764298cd1abad9e Mon Sep 17 00:00:00 2001
From: Samuel Klein <klein@bio.ifi.lmu.de>
Date: Thu, 23 Mar 2023 14:51:36 +0100
Subject: [PATCH] removed redundant code that sets the secondary alignment flag
 for a readpair

---
 src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java b/src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
index 310e967f26..d1a48fa997 100644
--- 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);