From f859e14cc727628f98328bc85ffceeb88d620c65 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Feb 2010 20:46:16 +0000
Subject: [PATCH] Allow no-call alleles to propagate through to the MAF file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2848 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/maf_annotation/vcf_to_germline_maflite.pl | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/perl/maf_annotation/vcf_to_germline_maflite.pl b/perl/maf_annotation/vcf_to_germline_maflite.pl
index 437c24606..e767fc71c 100755
--- a/perl/maf_annotation/vcf_to_germline_maflite.pl
+++ b/perl/maf_annotation/vcf_to_germline_maflite.pl
@@ -22,16 +22,20 @@ while (defined($line = <STDIN>)) {
         $allele1 = $ref;
     } elsif ($geno1 eq "1") {
         $allele1 = $alt;
+    } elsif ($geno1 eq ".") {
+        # do nothing - just leave the N in place
     } else {
-        die("only handled single alt currently:\n$line \n");
+        die("allele1: only handled single alt currently:\n$line \n");
     }
 
     if ( $geno2 eq "0") { 
         $allele2 = $ref;
     } elsif ($geno2 eq "1") {
         $allele2 = $alt;
+    } elsif ($geno2 eq ".") {
+        # do nothing - just leave the N in place
     } else {
-        die("only handled single alt currently:\n$line\n");
+        die("allele2: only handled single alt currently:\n$line\n");
     }
 
     my $ncbiBuild = "36";