If @fix is only used in that loop consider removing it.

  for my $i (0 .. $chrsize{$chr}) {
    $index{$k} = "$chr\t$i";
    $score[$k] = $piRNA{$chr}{$i} - $penalty;  
    
    if ( defined $breakpoint{$chr}{$i} 
         && $breakpoint{$chr}{$i}==1 ){
      $S[$k] = 0;
    } else {
      if ($i == 0) {
        $S[$k] = $score[$k];      
      } else {
        $S[$k] = $S[$k-1]+$score[$k];
      }   
      $S[$k] = 0 if $S[$k]<0;
    }
    $k++;
  }
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