#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;

my @chrom;

while (<>) {
    my ($chr, $start,$end,$c,$d,$strand)= split;
    push @chrom, {'chrom'=>$chr, 'start'=>$start, 'end'=>$end, 'strand'=>$strand };

}
my @chroms= sort { $a->{start} <=> $b->{start} } @chrom;

#print Dumper(\@chroms);

exit(0) if (@chroms==0);
my $coord= shift @chroms; #use first coordinate as range counter
my $overlap=1;
my $id= 1;

while( my $co= shift @chroms ) {
    if ($co->{chrom} ne $coord->{chrom}) {
	printresults($coord,$overlap,$id);
	$coord= $co;
	$overlap=1;
	$id=1;
    }
    else {
	if ($co->{start}>=$coord->{end}) {
	    printresults($coord,$overlap,$id);
	    $coord= $co;
	    $overlap=1;
	    $id++;
	}
	else {
	    $overlap++;
	    $coord->{end}= $co->{end};
	}
    }
}

printresults($coord,$overlap,$id);



#-------------

sub printresults {
    my ($coord,$overlap,$id)= @_;
    print "ID_$id       $coord->{chrom}      $coord->{start}     $coord->{end}    $coord->{strand}      $overlap\n";
}