#! perl -slw
use strict;
use Time::HiRes qw[ time ];

sub mem{ 
    my( $mem ) = `tasklist /nh /fo csv /fi \"pid eq $$\"` 
        =~ m[\"([\d,]+\s+.)\"$]; 
    $mem 
}

our $FUZZ	||=  2;
our $KEYLEN ||= 25;
our $MEM	||= 0;

die "Need two files" unless @ARGV == 2;

my $start = time();

open FRAGS, '<', $ARGV[ 0 ] or die "$ARGV[ 0 ] : $!";
chomp( my @fragments = <FRAGS> );
close FRAGS;

# initialization code
my $chunks = join ")(", 
	map "."x ( int(   $_       * $KEYLEN / ( $FUZZ + 1 ) ) 
	         - int( ( $_ - 1 ) * $KEYLEN / ( $FUZZ + 1 ) ) )
	, 1 .. $FUZZ + 1;
my $qr = qr/(?=(($chunks)))./;

my @filters;
for my $frag ( @fragments ) {
	my @m = $frag =~ $qr
		or die "something's horribly wrong, $frag =~ $qr ";
	push @{ $filters[$_]{ $m[ $_ ] } }, $frag for 1..$#m;
}

open SEQ, '<', $ARGV[ 1 ] or die "$ARGV[ 1 ] : $!";

my $empty = [];
my $count = 0;
# search code
while( my $seq = <SEQ> ) {
	while( $seq =~ /$qr/g ) {
		my %uniq;
		for ( map @{ 
                $filters[ $_ - 1 ]{ substr $seq, $-[$_], $+[$_]-$-[$_] } 
                || $empty 
            }, 2..$#- ) {
			if ( ( $1 ^ $_ ) =~ tr/\0//c <= $FUZZ && !$uniq{ $_ }++ ) {
				++$count;
				printf "line:$. offset:%d fuzz: %d '%s'\n", $-[ 0 ], 
                    ( ( $1 ^ $_ ) =~ tr/\0//c ), $_;
			}
		}
	}
}
my $elapsed = time() - $start;
close SEQ;
warn "Found $count matches in (secs): ", $elapsed, 
    ( $MEM ? ' Mem: ' . mem() : () ), $/;