gistfile1.pl

#!/usr/bin/env perl

use strict;
use warnings FATAL => 'all';

use List::Util qw(max min);

my @COLS     = qw( label _ chr strand start end );
my @KEY_COLS = qw( label chr strand );

my %refSeq;

while (<>) {
    chomp;
    my %h;
    @h{@COLS} = split "\t";
    my $key = join ':', @h{@KEY_COLS};
    if ( $refSeq{$key} ) {
        $refSeq{$key}{start} = min( $refSeq{$key}{start}, $h{start} );
        $refSeq{$key}{end}   = max( $refSeq{$key}{end}, $h{end} );
    }
    else {
        $refSeq{$key} = \%h;
    }
}

for ( sort { $a->{chr} cmp $b->{chr} || $a->{start} <=> $b->{start} || $a->{end} <=> $b->{end} } values %refSeq ) {
    print join( "\t", @{$_}{@COLS} ) . "\n";
}