use threads ;
use feature "say";
#use strict;
use warnings;


`tr -d '\n' </home/guru/Desktop/sequence.fasta >modified_human_chr_1.txt`;

my $input_file = "modified_human_chr_1.txt";
open my $hd, "<", $input_file or die "Couldn't open '$input_file' - $!";
my $text=<$hd>;
chomp($text);

my $window=5;
my $i=0;
LOOP:seek $hd,$i,0;
read ($hd,my $substring,$window);
my %hash;
if(length($substring)==$window)
{
	$hash{$substring}=$i;
	$i++;
	goto LOOP;
}

my $count = keys %hash;
my $j=0;

foreach my $pattern (keys %hash)
{
	if($j<=$count)
	{
		my $thr="thread".$j;
		$$thr=threads->create(\&hunter,$text,$pattern);
		
		$j++;
	}
}

my @returns;

foreach $thread (threads->list) 
{
   	if ($thread->is_joinable() ) {  push @returns, $thread->join; }
   	if( scalar (threads->list) == 0 ) {last;} 
}

print "@returns\n";

sub hunter
{
	my ($text,$pattern) = @_ ;
	
	my $offset = 0;

	print "\n$pattern ($window)\n";
	print '~' x $window,"\n";
	
	my $pos=index $text,$pattern,$offset;
	
	while ($pos != -1) 
	{
		print $pos+1," to ",$pos+$window,"\n";
		$offset = $pos + 99;
    	$pos = index($text, $pattern, $offset);
    }
}