From 2235eedb122236c7b25d38adfdec55380defe1d4 Mon Sep 17 00:00:00 2001
From: Cyriac Kandoth <ckandoth@gmail.com>
Date: Mon, 29 Mar 2021 14:29:26 -0700
Subject: [PATCH] maf2maf: Remove only one anchor bp if found, not all of them

---
 maf2maf.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/maf2maf.pl b/maf2maf.pl
index 213629c..7c24e66 100644
--- a/maf2maf.pl
+++ b/maf2maf.pl
@@ -274,8 +274,8 @@
             # Prefer Tumor_Seq_Allele2 over Tumor_Seq_Allele1 if both are non-REF
             my $var = (( defined $al2 and $al2 and $al2 ne $ref ) ? $al2 : $al1 );
 
-            # Remove any prefixed reference bps from alleles, using "-" for simple indels
-            while( $ref and $var and substr( $ref, 0, 1 ) eq substr( $var, 0, 1 ) and $ref ne $var ) {
+            # Remove (only one) prefixed reference bp from alleles, using "-" for simple indels
+            if( $ref and $var and substr( $ref, 0, 1 ) eq substr( $var, 0, 1 ) and $ref ne $var ) {
                 ( $ref, $var ) = map{$_ = substr( $_, 1 ); ( $_ ? $_ : "-" )} ( $ref, $var );
                 ++$pos unless( $ref eq "-" );
             }