start	end	ID
36701	40200	1
37901	39700	2
36701	39700	3


##</code><code>##

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

#get the scaffold file name from user input (@ARGV) and stores in $file
#opens the scaffold file so that it can be used to fill the empty interval tree
my $file = shift;
open my $fh, '<', $file or die "Cannot open $file: $!";


#create an empty interval tree
my $tree = Set::IntervalTree -> new();


#loop to the file, read each line and add objects to the empty interval tree
#there will be as many objects in the interval tree as there are hits for the specific file

my %overlap_table;

while (my $line=<$fh>){                      #while there are lines

      my @low = split("\t", $line);   #get the <code> value from the 1st column (start position = low BT)
                                print "$low[0]\n";
        $overlap_table{$low[0]}++;


        my @high = split("\t", $line);  #get the value from the 2nd column (end position = high BT)
                              print "$high[1]\n";
      $overlap_table{$high[1]}++;


       my @ID = split ("", $line);     #ID information is the "value"
                              print "$ID[2]\n";
      $overlap_table{$ID[2]}++;
                       }

close($fh);
 print Dumper \%overlap_table;