#! perl -slw
use strict;
use bytes;

our $FUZZY ||= 4;

open KEYS, '<', $ARGV[ 0 ] or die "$ARGV[ 0 ] : $!";
my @keys = <KEYS>;
close KEYS;
chomp @keys;
warn "Loaded ${ \scalar @keys } keys";
my $seq ;
my $seqnam;
readseqfile();
my( $masked, $pos );

my $totalLen = 0;
my $count = 0;

	my $seqLen = length $seq;
	$totalLen += $seqLen;
	for my $key ( @keys ) {
		my $keyLen     = length $key;
		my $mask       = $key x ( int( $seqLen / $keyLen ) + 1 );
		my $maskLen    = length $mask;
		my $minZeros   = chr( 0 ) x int( $keyLen / ( $FUZZY + 1 ) );
		my $minZlen	   = length $minZeros;
		for my $offset1 ( 0 .. $keyLen-1 ) { 

			$masked =  $mask ^ substr( $seq, $offset1, $maskLen );
			$pos = 0;
			while( 
				$pos = 1+index  $masked, $minZeros, $pos 
			) {
				$pos--;
				my $offset2 = $pos - ($pos % $keyLen );
				last unless $offset1 + $offset2 + $keyLen <= $seqLen;
				
				my $fuz = $keyLen 
					- ( substr( $masked, $offset2, $keyLen ) =~ tr[\0][\0] );
				if( $fuz <= $FUZZY ) {
					#printf "\tFuzzy matched key:'$key' -v- '%s' in line:"
					#	.  "%2d @ %6d (%6d+%6d) with fuzziness: %d\n", 
					#	substr( $seq, $offset1 + $offset2, $keyLen ),
					#	$., $offset1 + $offset2, $offset1, $offset2, $fuz;
				}
				$pos = $offset2 + $keyLen;
			}
		}
	}

warn "\n\nProcessed $. sequences";
warn "Average length: ", $totalLen / $.;

    sub readseqfile {
        open( SEQ, "<$ARGV[1]" );
        while (<SEQ>) {
            chomp();
            if (/>(\S+)/) {

                $seqnam = $1;
                $seq = "";
            }
            else {
                $seq .= $_;
            }
        }
        close SEQ;
    }