my %file1;
while(<INPUT1>){
	chomp;
	(my $id, my $number) = split /\t/;
	
	if ($id=~ m/^(CLS_S3_Contig[0-9]+)([-]?)([0-9]+)([_]?)([0-9]+)$/i) {
		$file1{$1} = [$3-8, $5+7]; # or should it be $5+8?
	}
}
print "Processed $. lines from $ARGV[0] file\n";
close(INPUT1);

##</code><code>##

while(<INPUT2>){
	chomp;
	my @current_line  = split /\t/;
	
	# eliminate unqualified lines early
	next unless $current_line[2] ==1 && $current_line[3] >= 3;
	
	if ($file1{ $current_line[0]}) {
		my ($lo, $hi) = @{ $file1{ $current_line[0] } };
		if ($lo <= $current_line[1] && $current_line[1] <= $hi) {
			print join("\t", $_, "***", $current_line[1]), "\n";
		}
	}
}

close (INPUT2);

##</code><code>##

	# eliminate unqualified lines early
	next unless $current_line[2] ==1 && $current_line[3] >= 3;