From 9e26c165501ced20e62cb46c1a432b1e73822a38 Mon Sep 17 00:00:00 2001
From: fa8sanger <fa8@sanger.ac.uk>
Date: Tue, 2 Apr 2024 12:04:59 +0100
Subject: [PATCH] Update indelCaller_step2.pl - minor fix for mitochondrial
 genome (circular chr). If start <= 0 set it to 1

---
 perl/indelCaller_step2.pl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/perl/indelCaller_step2.pl b/perl/indelCaller_step2.pl
index 377df21..c317ffb 100755
--- a/perl/indelCaller_step2.pl
+++ b/perl/indelCaller_step2.pl
@@ -212,6 +212,9 @@ sub runCmd {
 
   print STDOUT "Step 3...\n";
   #`samtools mpileup --no-BAQ  -d 250 -m 2 -F 0.5 -r $chr:$start-$end --BCF --output-tags DP,DV,DP4,SP -f $ref_genome -o $tempdir/$out_name.bcf $tempdir/$out_name.tmp.bam`;
+  if($start <= 0) {
+	$start = 1;
+  }
   &runCmd("bcftools mpileup --no-BAQ  -L 250 -m 2 -F 0.5 -r \"$chr:$start-$end\" -O b -a DP,DV,DP4,SP -f $ref_genome -o $tempdir/$out_name.bcf $tempdir/$out_name.tmp.bam");
   
   print STDOUT "Step 4...\n";