#!/usr/bin/perl
use strict;
use warnings;
use Set::IntSpan;

my $cnv = <<EOF;
start   stop  size(in bp)
5389769	98256008	3567
7452344	871875466	64547
EOF

my $genelist1 = <<EOF;
name start stop
BRCA1	41196312	41277500
TP53	7571720	7590863
EOF

my $genelist3 = <<EOF;
name start stop
OMG	29621668	29624380
NR3C1	142657496..142815077
EOF

my @cnv;
open my $fh, "<", \$cnv;
<$fh>; # toss header
while (<$fh>) {
	chomp;
	my ($start, $stop, $size) = split /\t/;
	push @cnv, { span => Set::IntSpan->new("$start-$stop"),
				 size => $size,
			   };
}
close $fh or die $!;

printf "%-10s%10s%10s%10s\n", ('gene name', qw/ size start stop /);
for (\$genelist1, \$genelist3) {
	open $fh, "<", $_;
	<$fh>; # toss header
	while (<$fh>) {
		chomp;
		my ($name, $start, $stop) = split /\t|(?<=\d)\.\.(?=\d)/;
		
		my $span = Set::IntSpan->new("$start-$stop");
		
		for my $href (@cnv) {
			my $intersect = $span->intersect( $href->{span} );
			if ($intersect) {
				printf "%-10s%10s%10s%10s\n",
					$name, $href->{size}, $intersect->min, $intersect->max;
			}
		}
	}
	close $fh or die $!;
}