use strict;
use diagnostics;
use warnings;

my $pt;
my $ct;
my $i;
my $j;
my $debug_distance = 0;

open (PT, "<$ARGV[0]");
$pt = <PT>;
close (PT);

open (CT, "<$ARGV[1]");
$ct = <CT>;
close (CT);

if (defined $ARGV[2])
{
    $debug_distance = $ARGV[2];
}

if (length($pt) != length ($ct))
{
    print "The pt and ct are different lengths, aborting\n";
}

my $position = 0;
my $len = length ($pt);
my %map;
my %distance;

while ($position < $len)
{
    my $p = substr ($pt, $position, 1);
    my $c = substr ($ct, $position, 1);

    if (($p ne "?") && ($c ne "?"))
    {
        if (defined $map{$p . $c})
        {
            # We encountered this pair already, calculate the distance
            my $d = sprintf "%5d", $position - $map{$p . $c};
            
            if (defined $distance { $d })
            {
                ++$distance { $d };
            }
            else
            {
                $distance { $d } = 1;
            }
            
            if ($d == $debug_distance)
            {
                # Display all $position values for the debug distance
                printf "DEBUG: distance %7d occurred at positions %7d and %7d\n", $debug_distance, $map{$p . $c}, $position;
            }
        }
        
        $map {$p . $c} = $position;
    }

    ++$position;
}

printf "\n\n";
print "pt/ct identity distances not encountered\n";
print "----------------------------------------\n";
my $lim = $len < 1000 ? $len : 1000;

for (my $i=1; $i<$lim; $i++)
{
    my $key = sprintf "%5d", $i;
    if (!(defined $distance{$key}))
    {
        printf "\tDistance of %5d not encountered\n", $i;
    }
}

print "\n";
print "pt/ct identity distances and counts\n";
print "-----------------------------------\n";
foreach my $key (sort keys %distance)
{
    printf "\t%05d\t%05d\n", $key, $distance{$key};
}