From 0212cf79750e9b32aaf0fdaa7025edbeb2e7860b Mon Sep 17 00:00:00 2001
From: fa8sanger <fa8@sanger.ac.uk>
Date: Tue, 2 Apr 2024 12:06:23 +0100
Subject: [PATCH] Update indelCaller_step2.pl

---
 perl/indelCaller_step2.pl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/perl/indelCaller_step2.pl b/perl/indelCaller_step2.pl
index 377df21..b250a7a 100755
--- a/perl/indelCaller_step2.pl
+++ b/perl/indelCaller_step2.pl
@@ -177,6 +177,7 @@ sub runCmd {
 print STDOUT "\ntmp dir : $tempdir\n\n";
 foreach my $rb_id (keys %indels) {
   my($chr,$start,$end) = (split(/,/,$rb_id))[0,1,2];
+  if($start <= 0) {	$start = 1;	}
   my(%good_sites,%bad_sites);
   foreach my $pos ( keys %{$indels{$rb_id}} ) {
     if($indels{$rb_id}->{$pos}->{"sw"} == 0 && $indels{$rb_id}->{$pos}->{"snp"} == 0) {