@ARGV or die "No input file specified";

open my $first,  '<', $ARGV[0] or die "Unable to open input file: $!";
open my $second, '<', $ARGV[1] or die "Unable to open input file: $!";

print scalar(<$first>);

my $secondHeader = <$second>;

while (<$first>) {
    @cols = split /\s+/;
    $p1   = $cols[1]; 
    $p2   = $cols[2]; 

    my $secondLine = <$second>;
    if ( defined $secondLine ) {
        @sec = split( /\s+/, $secondLine );
		print join( "\t", @cols ), "\n" if ( $p1>=$sec[0] && $p2<=$sec[1] || $p1<=$sec[0] && $p2>=$sec[1] ); 
    }
}