From 25161f800d273c3f94e0a31d682e99834ccb4b01 Mon Sep 17 00:00:00 2001
From: Cyriac Kandoth <ckandoth@gmail.com>
Date: Sun, 1 Nov 2015 18:01:40 -0500
Subject: [PATCH] Support buggers who dunno how to convert hg19 to grch37

---
 maf2vcf.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/maf2vcf.pl b/maf2vcf.pl
index baaaea7..84ce0dd 100644
--- a/maf2vcf.pl
+++ b/maf2vcf.pl
@@ -142,8 +142,8 @@
 
     # Make a version of chrom without chr-prefixes, and chrM renamed to MT
     my $no_prefix_chr = $chr;
-    $no_prefix_chr =~ s/chrM/MT/;
     $no_prefix_chr =~ s/^chr//;
+    $no_prefix_chr =~ s/^M$/MT/;
     
     # To represent indels in VCF format, we need to fetch the preceding bp from a reference FASTA
     my ( $ref_len, $al1_len, $al2_len ) = map{( $_=~m/^(\?|-|0)+$/ ? 0 : length( $_ )) } ( $ref, $al1, $al2 );