From 3d14a0e3501680aaeff1ea208c35b5d0e9319a95 Mon Sep 17 00:00:00 2001
From: RaphaelRaphael <raphael.poujol@gmail.com>
Date: Tue, 30 Apr 2024 17:03:27 -0400
Subject: [PATCH] This modification allow the final file to contain the true
 reference #7

---
 pileup2baseindel.pl | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/pileup2baseindel.pl b/pileup2baseindel.pl
index 7dadecb..084ca1a 100644
--- a/pileup2baseindel.pl
+++ b/pileup2baseindel.pl
@@ -72,7 +72,7 @@
 	
 	my @region=(3*($i-1),3*($i-1)+1,3*($i-1)+2);
 	my ($dp,$bases,$bq) = @dp_bases_bq[@region];
-	my $str = parsePileup($bases,$bq,$BQcut,$offset);
+	my $str = parsePileup($bases,$bq,$BQcut,$offset,$ref);
 	
 	if($str ne "*"){
 		print $fh join "\t",($chr,$loc,$ref,$str);
@@ -88,7 +88,7 @@
 		my $fh = $files{$i};
 		my @region=(3*($i-1),3*($i-1)+1,3*($i-1)+2);
 		my ($dp,$bases,$bq) = @dp_bases_bq[@region];
-		my $str = parsePileup($bases,$bq,$BQcut,$offset);
+		my $str = parsePileup($bases,$bq,$BQcut,$offset,$ref);
 		if($str ne "*"){
 			print $fh join "\t",($chr,$loc,$ref,$str);
 		}
@@ -103,7 +103,7 @@
 
 
 sub parsePileup{
-	my ($bases,$bq,$BQcut,$offset) = @_;
+	my ($bases,$bq,$BQcut,$offset,$ref) = @_;
 	
 	if($bases eq "*"){
 		return "*";
@@ -158,7 +158,6 @@ sub parsePileup{
 	my $reverse_T=0;
 	my $reverse_C=0;
 	my $reverse_G=0;
-
 	#start the loop
 	for(my $i=0;$i<@base;$i++){
 		my $ch=$base[$i];
@@ -226,4 +225,3 @@ sub parsePileup{
 	$str.=$insertion."\t".$deletion."\n";
 	return $str;
 }
-