From e9af893bf458bacbef547c50ac0e1421eb25b7c3 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Sep 2010 23:46:27 +0000
Subject: [PATCH] Write headers that are VCF4.0 compliant

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4213 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/AnnotateVCFwithMAF.pl | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/perl/AnnotateVCFwithMAF.pl b/perl/AnnotateVCFwithMAF.pl
index 9603dc6e5..cd17060b9 100755
--- a/perl/AnnotateVCFwithMAF.pl
+++ b/perl/AnnotateVCFwithMAF.pl
@@ -1,6 +1,7 @@
 #!/usr/bin/perl -w
 
 use strict;
+use Data::Dumper;
 
 sub usage {
     print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n";
@@ -62,16 +63,17 @@ while (my $vcfline = <VCF_IN>) {
     if ($vcfline =~ /##/) {
         print VCF_OUT "$vcfline\n";
     } elsif ($vcfline =~ /#CHROM/) {
+
         print VCF_OUT "##source=AnnotateVCFwithMAF\n";
-        print VCF_OUT "##INFO=cDNAchange,1,String,cDNAchange\n";
-        print VCF_OUT "##INFO=classification,1,String,classification\n";
-        print VCF_OUT "##INFO=codonchange,1,String,codonchange\n";
-        print VCF_OUT "##INFO=gene,1,String,gene\n";
-        print VCF_OUT "##INFO=genomechange,1,String,genomechange\n";
-        print VCF_OUT "##INFO=proteinchange,1,String,proteinchange\n";
-        print VCF_OUT "##INFO=strand,1,String,strand\n";
-        print VCF_OUT "##INFO=transcript,1,String,transcript\n";
-        print VCF_OUT "##INFO=type,1,String,type\n";
+        print VCF_OUT "##INFO=<ID=cDNAchange,Number=1,Type=String,Description=\"cDNAchange\">\n";
+        print VCF_OUT "##INFO=<ID=classification,Number=1,Type=String,Description=\"classification\">\n";
+        print VCF_OUT "##INFO=<ID=codonchange,Number=1,Type=String,Description=\"codonchange\">\n";
+        print VCF_OUT "##INFO=<ID=gene,Number=1,Type=String,Description=\"gene\">\n";
+        print VCF_OUT "##INFO=<ID=genomechange,Number=1,Type=String,Description=\"genomechange\">\n";
+        print VCF_OUT "##INFO=<ID=proteinchange,Number=1,Type=String,Description=\"proteinchange\">\n";
+        print VCF_OUT "##INFO=<ID=strand,Number=1,Type=String,Description=\"strand\">\n";
+        print VCF_OUT "##INFO=<ID=transcript,Number=1,Type=String,Description=\"transcript\">\n";
+        print VCF_OUT "##INFO=<ID=type,Number=1,Type=String,Description=\"type\">\n";
         print VCF_OUT "$vcfline\n";
 
         $vcfline =~ s/#//g;
@@ -110,7 +112,11 @@ while (my $vcfline = <VCF_IN>) {
 
         my @newinfo;
         foreach my $infokey (sort { $a cmp $b } keys(%info)) {
-            push(@newinfo, "$infokey=$info{$infokey}");
+            if (!defined($info{$infokey})) {
+                #print "$infokey is missing\n";
+            } else {
+                push(@newinfo, "$infokey=$info{$infokey}");
+            }
         }
         $vcfentry{'INFO'} = join(";", @newinfo);