add_prefix_chr_to_chromosome_names

#!/usr/bin/perl -w

use warnings;
use strict;
use POSIX;
use Getopt::Long;
use File::Path;
use File::Basename;
use Pod::Usage;

=head1 NAME

add_prefix_chr_to_chromosome_names

=head1 SYNOPSIS

 add_prefix_chr_to_chromosome_names [options]  
  
=head1 DESCRIPTION
 
 Adds chr prefix to chromosome names.  
 
=cut

#option variables
my $help;
my $verbose;
my $debug;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions ('h'=>\$help, 'v'=>\$verbose, 'd'=>\$debug) 
  || scalar(@ARGV)!=1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

my $inputVCFFile = $ARGV[0];

if ($inputVCFFile ne "-")
{
    open(VCF, $inputVCFFile);

    while(<VCF>)
    {
        chomp;
        
        if (/^#/)
        {
            if (/^##contig=<ID=/)
            {
                s/ID=/ID=chr/;
            }
            
            print "$_\n";
        }
        else
        {
            print "chr$_\n";
        }
    }
    
    close(VCF);
}
else
{
    while(<STDIN>)
    {
        chomp;
        
        if (/^#/)
        {
            if (/^##contig=<ID=/)
            {
                s/ID=/ID=chr/;
            }
            
            print "$_\n"; 
        }
        else
        {
            print "chr$_\n";
        }
    }    
}