sub index_file {
    my %params = @_;

    my $hashref = exists($params{hashref}) ? $params{hashref} : {};
    my $file = $params{file};
    my $window = $params{window};
    
    open(INF,$file) or die "Cannot open file $file : $!";
    
    print "Reading file....\n";
    my $sequence;
    while (my $line = <INF>) {
      chomp($line);
      $sequence .= $line unless ($line=~/^>.*/);
    }
    close(INF);
    $sequence =~ tr/a-z/A-Z/;
    $sequence =~ s/N//g;
    
    my $offset=0;
    print "Calculating....\n";
    for ($offset=0;$offset<length($sequence)-$window;$offset++) {
      print "$offset\n" if ($offset % 10000000 ==0); 
      $hashref->{substr($sequence,$offset,$window)}++;
    }
    
    return($hashref);
}