#!/usr/bin/perl


# extract command line arguments
@indivs = @ARGV;

# remove command line arguments (so while(<>) works)
foreach $argnum (0 .. $#ARGV) {
    $test=shift @ARGV;
}


# Header line 1, shows first person comparison
printf "%-12s", "P1 vs. P2";

for($c1=0;$c1<(@indivs+0);$c1++) {
    printf "%3s", "";
}
for($c1=0;$c1<(@indivs+0);$c1++) {
    printf "%3s", $indivs[$c1];
    for($c2=0;$c2<(@indivs-1);$c2++) {
	if ($c2+1==$c1){
	    printf "%3s", "*";
	}
	else{
	    printf "%3s", "";
	}
    }
}

print "\n";

# Header line 2, shows second person comparison
printf "%-12s", "marker";

for($c1=0;$c1<(@indivs+0);$c1++) {
    printf "%3s", $indivs[$c1];
}
for($c1=0;$c1<(@indivs+0);$c1++) {
    for($c2=0;$c2<(@indivs+0);$c2++) {
	printf "%3s", $indivs[$c2];
    }
}

print "\n";


while(<>){
    ($marker, @genotypes) = split(/\s/,$_);
    printf "%-12s", $marker;
    ## number of genotypes
    #print "(".(@genotypes)." genotypes):";
    %counts = ("AA/TT",0,"AC/TG",0,"AG/TC",0,"CC/GG",0,"--/--",0);
    for($c1=0;$c1<(@indivs+0);$c1++) {
	$gt = $genotypes[$indivs[$c1]];
	if ($gt =~ /(aa|tt)/i){
	    printf "%3s", "aa";
	}
	elsif ($gt =~ /(ac|ca|tg|gt)/i){
	    printf "%3s", "ac";
	}
	elsif ($gt =~ /(ag|ga|tc|ct)/i){
	    printf "%3s", "ag";
	}
	elsif ($gt =~ /(cc|gg)/i){
	    printf "%3s", "cc";
	}
	elsif ($gt =~ /../) {
	    printf "%3s", "--";
	}
	else{
	    printf "%3s", "??";
	}
    }
    for($c1=0;$c1<(@indivs+0);$c1++) {
	for($c2=0;$c2<(@indivs+0);$c2++) {
	    $gt1 = $genotypes[$indivs[$c1]];
	    $gt2 = $genotypes[$indivs[$c2]];
	    if ($gt1 =~ /(aa|tt)/i && $gt2 =~ /(aa|tt)/i){
		printf "%3s", "1";
	    }
	    elsif ($gt1 =~ /(ac|ca|tg|gt)/i && $gt2 =~ /(ac|ca|tg|gt)/i){
		printf "%3s", "1";
	    }
	    elsif ($gt1 =~ /(ag|ga|tc|ct)/i && $gt2 =~ /(ag|ga|tc|ct)/i){
		printf "%3s", "1";
	    }
	    elsif ($gt1 =~ /(cc|gg)/i && $gt2 =~ /(cc|gg)/i){
		printf "%3s", "1";
	    }
	    # if genotypes are not similar, then don't consider similar
	    else {
		printf "%3s", "0";
	    }
	}
    }
    print "\n";
}