I have input file with these kind of data : 
 chr            start        end
chr21   9411509 9411529
chr21   9411510 9411529
chr21   9411509 9411529
chr21   9411569 9411589
chr21   9411571 9411591
chr21   9411572 9411592
chr21   9411573 9411593
chr21   9411575 9411595
chr21   9411578 9411598

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I want to have output which counting the number of overlapped between 1st position in start and end position with 2bp overlap : Imagine the start pos of the clusters are and end of them could have over lap with 2bp like the pic at the bottom and it counts 4 
|-----|
    |-----|
          |-----|
   |------|

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and if it does not have overlap like : do not count it and give each of them one ID which are not overlapped 
|----|
      |----|
           |-----|
                    |-----|

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and get output like this 
TSSD_ID  Start position End  position  Count overlapped
ID_1        XXXXX               XXXXXX          54

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I make the script but It's not work well : 
#!/usr/bin/perl -w

use strict;
use warnings;
my $data = <>;
my $tol  = 2;
my @chr; 
my @start;
my @end;
my @count;
my @strand;
while ( $data = (<>) ) {
    my (
        $chr,        $start,   $end,      $info,
        $cnt, $strand, $start2, $end2,
        $color,   $cnt2, $length , $zero
      )
      = split( "\t", $data );
    push( @chr, $chr);
push (@start, $start);
push (@end, $end);
push (@strand, $strand);
}
my $cl1length = @start;
my $cl2length = @end;
print "TSSD_ID \t Start \t End \t Count\t Strand \n" ;
foreach ( my $i =0 ; $i < $cl1length ; $i = $i++) {
    for ( my $i = 1 ; $i < $cl1length ; $i++ ) {
my $ID = 1;    
my $count = 0;
for (my $j = 0 ; $j < $cl2length ; $j++) {
    if ( $tol < ( $start[$i] - $start[$i+1] ) ) { $ID++; }
if ($start[$i]-$start[$j] == 0) { $count++;}}
    print  "ID_$ID \t $chr[$i] \t $start[$i] \t $end[$i] $count \t $st
+rand[$i]  \n"; }}

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what should i do?! :(

In reply to Help the counting! by g-alone

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