$file = shift;

print "Window length\n";
$kmer = <STDIN>;
chomp ($kmer);

print "Minimum quality score cut-off\n";
$cut_off = <STDIN>;
chomp ($cut_off);

open (MYFILE, ">R.txt");

if (open (FASTQ, $file)) {
    while ($header1 = <FASTQ>) {
        $dna       = <FASTQ>;
        $header2   = <FASTQ>;
        $qual      = <FASTQ>;
        @dna       = split ('', $dna);
        @qual      = split ('', $qual);
        @num_value = ();
        @scores    = ();

        foreach $qscore (@qual) {
            $num_value = ord ($qscore) - 33;
            push (@num_value, $num_value);
        }

        foreach $value (@num_value) {
            if ($value < $cut_off) {
                pop (@qual);
            } else {
                last;
            }
        }
        $sub1  = substr ($dna,  -$#qual);
        $sub11 = substr ($qual, -$#qual);

        @qscopy = reverse @num_value;
        foreach $value (@qscopy) {
            if ($value < $cut_off) {
                pop (@qual);
            } else {
                last;
            }
        }
        $sub2  = substr ($sub1,  0, $#qual);
        $sub22 = substr ($sub11, 0, $#qual);

        for ($i = 0; $i <= $#qual - ($kmer - 1); $i++) {
            @scores = @num_value[$i .. $i + $kmer - 1];

            $sum = 0;
            foreach $score (@scores) {
                $sum += $score;
            }
            if (($sum / $kmer) < $cut_off) {
                last;
            }
        }
        $sub3  = substr ($sub2,  0, ($i - 1));
        $sub33 = substr ($sub22, 0, ($i - 1));

        print MYFILE "$header1$sub3\n$header2$sub33\n\n";
    }
} else {
    print "Error!\n";
}

close MYFILE;