open IN, '<', $ARGV[0];
my %hash1;
while (<IN>) {
    next unless ( $_ =~ m/^\@HWI/ );
    my ($header) = split(/ /, $_);
    $hash1{$header} = 1;   
}
close IN;

open IN2, '<', $ARGV[1];
my %hash2;
while (<IN2>) {
    next unless ( $_ =~ m/^\@HWI/ );
    my ($header) = split(/ /, $_);
    $hash2{$header} = 1;   
}
close IN;

##</code><code>##

my @threads = ("1","2");

# Loop through the array:
foreach(@threads){
    # Tell each thread to perform our 'parseLines()' subroutine.
    $_ = threads->create(\&parseLines, shift(@ARGV));
}

#Tries to join the running threads
#Some check implemented to avoid quitting the loop, before everything is joined
my @running = threads->list(threads::running); #Array of running threads
my @joinable = threads->list(threads::joinable); #Array of joinable threads
my @catcher;
while (scalar(@running) != 0 || scalar(@joinable) > 0) { #While as long as there are running or joinable threads
    @running = threads->list(threads::running); #Repopulate running, not sure if needed.
    foreach(@threads){
	if ($_->is_joinable()) {
	    push(@catcher, $_->join()); #Put's parsed file as hash-ref into array
	}
    }
    @joinable = threads->list(threads::joinable);
    @running = threads->list(threads::running);
}

sub parseLines{
    open IN, '<', $_[0];
    my %hash;
    while (<IN>) {
	next unless ( $_ =~ m/^\@HWI/ );
	my ($header) = split(/ /, $_);
	$hash{$header} = 1;   
    }
    close IN;
    return \%hash;
}