#var $cutoff defined earlier in script
open IN, "$filename.merged";
while (<IN>) {chomp; split(/\t/);
   if ($_[1] >= $cutoff){
      $_[0] =~/(chr.+):(\d+)-(\d+)/;
      foreach ($2..$3) {$breakpoint{$1}{$_}=1;}  #what is $_?
   }
}

##</code><code>##

open IN, "$filename.merged";
while (<IN>) {
   chomp(my $line= $_);
   my @array = split(/\t/, $line);
   if ($array[1] >= $cutoff){  # cutoff is defined earlier in original script
      $array[0] =~/(chr.+):(\d+)-(\d+)/;
      foreach ($2..$3) {$breakpoint{$1}{$_}=1;}  #would it be $line?