BrowserUk seems to answer these questions pretty well here.

Update: Actually, upon closer inspection, I think I would change the statement
    my( $start, $end ) = split "\t", $_;
in the  while( <INTERVAL> ) { ... } loop to
    my( undef, $start, $end ) = split "\t", $_;
because the interval data seems to be three-field, tab-delimited records like
chrX    1    60000
in which the first field, to be ignored, is a label of some kind.