c	8	336158	75	75M	74
c	12	828707	74	74M	73
w	10	528559	74	74M	0
c	15	267766	74	74M	73
c	12	828707	74	74M	73
c	14	491797	74	74M	73

##</code><code>##

	my @headers = split("\t",<$IN>);
	my $index = first{$headers[$_] eq 'Strand'} 0..$#headers;
	while (<$IN>) {
		chomp $_;
		my @F = split("\t", $_);
		if (exists $hits{$F[$index+1]}{$F[$index+2]}) {
		} else {
			$hits{$F[$index+1]}{$F[$index+2]}{'w'} = 0;
			$hits{$F[$index+1]}{$F[$index+2]}{'c'} = 0;
		}
		$hits{$F[$index+1]}{$F[$index+2]}{$F[$index]}++
	}


##</code><code>##

1	4	1	0
1	5	1	0
1	31	1	0
1	74	1	0
1	89	1	0
1	116	1	1
1	118	1	0
1	122	1	0
1	126	0	1
1	140	0	1
1	141	0	1
1	148	2	0
1	158	0	1
1	159	1	0