From 254ad33d95e43fc6fec6232ee7f9532a9a5f37d0 Mon Sep 17 00:00:00 2001
From: Anton Nekrutenko <anton@bx.psu.edu>
Date: Wed, 14 Apr 2010 13:52:35 -0400
Subject: [PATCH] Fixed indel calling in pileup wrapper. TO DO: Write a
 separate wrapper for indels only.

---
 tools/samtools/pileup_parser.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/samtools/pileup_parser.pl b/tools/samtools/pileup_parser.pl
index b3c9ee89827..27b4126d0a9 100755
--- a/tools/samtools/pileup_parser.pl
+++ b/tools/samtools/pileup_parser.pl
@@ -60,7 +60,7 @@ while (<IN>) {
 	my @qv    = split //, $base_quality;
 	
 	for my $base ( 0 .. @bases - 1 ) {
-		if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff )
+		if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff and $bases[ $base ] ne '*')
 		{
 			++$above_qv_bases;