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#var $cutoff defined earlier in script
open IN, "$filename.merged";
...
      foreach ($2..$3) {$breakpoint{$1}{$_}=1;}  #what is $_?
   }
}

open IN, "$filename.merged";
while (<IN>) {
...
   if ($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?