-w INT SNP within INT bp around a gap to be filtered [$opts{w}]
-W INT window size for filtering dense SNPs [$opts{W}]
- -N INT max number of SNPs in a window [$opts{W}]
+ -N INT max number of SNPs in a window [$opts{N}]
-l INT window size for filtering adjacent gaps [$opts{l}]
-p print filtered variants
-/) if (@ARGV == 0 && -t STDIN);
+\n/) if (@ARGV == 0 && -t STDIN);
# calculate the window size
my ($ol, $ow, $oW) = ($opts{l}, $opts{w}, $opts{W});