#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 $_?
   }
}