#! /usr/local/bin/perl

#  mapdist.pl: calculates total map length based on poisson
#  expectation for number of linked loci

# Steve DiFazio, 11-2002

use Getopt::Long;

GetOptions( "link:f" => \$link);

if(!($link)) {
    $link = 3;
}

if(!($ARGV[0])) { die "
_______________________________________________________________\n
Usage: perl mapdist.pl -l=<linkage cutoff> lod_table.txt > out.txt \n
where \t-<linkage cutoff> is the lod score cutoff for linkage,
\t<lod_table.txt> is the lod table output from mapmaker (with photo
\tmode activated)\n
** You can choose unique names for these input and output files **
_______________________________________________________________\n"; }

warn "\n";

while (<>) {
    if((/^\s+[0-9]/) && ($_ !~ />/)) {
	($n,@lod) = split(/\s+/);
	if($n>$maxn) {
	    $maxn = $n;
	}
	foreach my $i (0 .. $#lod) {
	    $comps++;
	    if(($lod[$i] ne "-") && ($lod[$i] >= $link)) {
		$links++;
	    }
	}
    }
}
# Divide total loci by 2 to account for repulsion phase alleles
print "Total Loci:\t",$maxn/2,"\n";
print "Comparisons:\t",$comps/4,"\n";
print "Linked Loci:\t$links\n";
print "LOD Cutoff:\t$link\n";