From be936eabf3acb0a5b581c6046bada9b6ab9b84fb Mon Sep 17 00:00:00 2001
From: Rob Davies <rmd+git@sanger.ac.uk>
Date: Fri, 13 Mar 2026 17:03:50 +0000
Subject: [PATCH] Move flags test in overlap_remove()

bam_plp_reset() calls overlap_remove() with the `b` parameter
set to NULL to make it clear out the overlap hash table.  This
means the tests on b->core.flag need to be in the `if (b)`
branch and not before.
---
 sam.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sam.c b/sam.c
index 966e855be..42327006b 100644
--- a/sam.c
+++ b/sam.c
@@ -5980,12 +5980,12 @@ static void overlap_remove(bam_plp_t iter, const bam1_t *b)
 {
     if ( !iter->overlaps ) return;
 
-    if ( b->core.flag&BAM_FUNMAP || !(b->core.flag&BAM_FPROPER_PAIR) ) //no need
-        return;
-
     khiter_t kitr;
     if ( b )
     {
+        if ( b->core.flag&BAM_FUNMAP || !(b->core.flag&BAM_FPROPER_PAIR) ) //no need
+            return;
+
         kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(b));
         if ( kitr!=kh_end(iter->overlaps) )
             kh_del(olap_hash, iter->overlaps, kitr);