#!/usr/local/bin/perl -w
# Verify that a list of marker indicies is really a clique.
#
# Copyright (C) 1995, 1996 Humberto Ortiz Zuazaga and Rosemarie Plaetke.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
#
# See the file licence.html for a copy of the GNU GPL

use strict;
use English;

my $minbrk = 3;

$minbrk = $ARGV[2] if $ARGV[2];

print "Verifying that all markers have at least $minbrk breaks.\n";

my @chrom = readchrom($ARGV[0]);
my @map = readmap($ARGV[1]);

my ($i, $j);
my $breaks;
my $chromosome;
my ($first, $second);

for $i (0..$#map) {
    for $j ($i+1..$#map) {
	$breaks = 0;
	foreach $chromosome (@chrom) {
	    $first = substr($chromosome, $map[$i] - 1, 1);
	    $second = substr($chromosome, $map[$j] - 1, 1);
	    if (($first ne $second) and ($first ne 'U') and ($second ne 'U')) {
		$breaks++;
	    }
	}
	if ($breaks < $minbrk) {
	    print "Marker $map[$i] has only $breaks breaks with marker $map[$j].\n";
	}
    }
}

###
sub readchrom {
    my ($filename) = @ARG;
    my ($markers, $chromosomes);
    my @chrom;
    my $line;

    open(CHROM, $filename) or die "readchrom: can't open $filename";
    $markers = <CHROM>;
    chomp $markers;
    print "Markers = $markers\n";
    for $i (1 .. $markers) {
	<CHROM>;
    }
    $chromosomes = <CHROM>;
    chomp $chromosomes;
    print "Chromosomes = $chromosomes\n";
    for $i  (0 .. $chromosomes - 1) {
	$chrom[$i] = <CHROM>;
	chomp $chrom[$i];
    }
    close CHROM;
    return @chrom;
}

###
sub readmap {
    my ($file) = @ARG;
    my $line;
    my @map;

    open(MAP, $file) or die "readmap: can't open $file";
    while ($line = <MAP>) {
	push @map, split ' ',$line;
    }
    return @map;
}