#initiate S for the whole genome
#chrboundst = chr start index
#chrbound = chr end index

my $k=0;
my @S=undef;
#open OUT, "> temp.0";
my %chrboundst;
my %index;  # correct?
my @fix;
my @score;
my %chrbound;
foreach my $chr (keys %chrsize) {
 $chrboundst{$chr}=$k;
 for (my $i=0; $i<=$chrsize{$chr}; $i++) {
     $index{$k}="$chr\t$i";
     $fix[$k]=1 if ($breakpoint{$chr}{$i}==1);  # line 132
     $score[$k]=$piRNA{$chr}{$i}-$penalty;
     $S[$k]=$S[$k-1]+$score[$k] if ($i>0);
     $S[$k]=$score[$k] if ($i==0);
     $S[$k]=0 if ($S[$k]<0 || $fix[$k]==1);  # line 136
     $k++;
     }
 $chrbound{$chr}=$k-1; # mark the chr end for recalculation
}