#!/usr/bin/perl
use warnings;
use strict;

my %total;
my $limit = 20;
while (<DATA>){
    chomp;
    my ($chr, $pos, $coverage) = split /\t/;
    $limit += 20 while $pos > $limit;
    

    # found a new limit and the hash has prior data
    # (i.e., not the case of the first record and no data in hash yet)
    if (! exists $total{$limit} && %total) {
        

        # there is only 1 key in the hash
        print join("\t", each %total), "\n";
        
        undef %total;
    }
    $total{$limit} += $coverage;
}

print join("\t", each %total), "\n";

__DATA__
chr    1    2
chr    4    2
chr    7    5
chr    22    5
chr    24    6
chr    38    10
chr    44    10
chr    50    20
chr    57    25
chr    60    30
chr    65    30
chr    105    30

[download]
Output 
20      9
40      21
60      85
80      30
120     30

[download]

Update: used the 'each' keyword to feed join

In reply to Re: How to calculate sum of a column by window size based on another column by Cristoforo
in thread How to calculate sum of a column by window size based on another column by rnaeye

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