#!/usr/bin/perl

# Copyright 2013 O. Sotolongo <osotolongo@fundacioace.com>

use strict; use warnings;
use Parallel::ForkManager;
use File::Slurp qw(read_file);
use File::Remove 'remove';
use File::Basename qw(basename);
use Data::Dump qw(dump);

my $debug = 1;

#my $library = '/home/data/GNlib/1000Genome/CEU_all/1000genome_CEU_merged.map';
my $library = '/home/osotolongo/data/GNlib/1000Genome/EUR/1000genome_eur.bim';

my $db = shift;
die "Must supply database\n" unless $db;
my $odb = $db;
$odb =~ s/(.*)\.(.*)/$1_freshed\.$2/;

print "I will try to write results to $odb\n";

my %genmap;
my %data_line = reverse map {/^(.*\s+(rs\d+)\s+.*)$/} grep {/^(.*\s+(rs\d+)\s+.*)$/} read_file $db;
print "Data stored, lets try to understand it\n";
foreach my $marker (sort keys %data_line){
	(@{$genmap{$marker}} {qw/chr data position/}) = $data_line{$marker} =~ /^(\d+)\s+rs\d+\s+(.*)\s+(\d+)$/;
}

print "Data read, lets work now\n";
open(IN, "<$library") || die "can't open $library";
while(<IN>){
	if (my ($libmarker, $libpos) = /^\d+\s+(rs\d+)\s+.*\s+(\d+)\s+.*/){ 
		if(exists $genmap{$libmarker}) {
			$genmap{$libmarker}{position} = $libpos;
		}
	}
}
close IN;

print "Writing to $odb\n";
open ODF, ">$odb" || die "Could not open output file";
foreach my $marker (sort {($genmap{$a}->{chr} <=> $genmap{$b}->{chr}) or ($genmap{$a}->{position} <=> $genmap{$b}->{position})} keys %genmap){
	print ODF "$genmap{$marker}{chr}\t$marker\t$genmap{$marker}{data}\t$genmap{$marker}{position}\n";
}
close ODF;