n50_cmdline.yaggo

purpose "Compute statistics on fasta"

description <<EOS
If no -N or -E switch is passed, it computes the N50. Otherwise
compute all the statistics asked for. The E-size is always displayed
last.
EOS

option("H", "no-header") {
  description "Do not display header"
  off }
option("a", "all") {
  description "All statistics and N50 if not other Nx specified"
  off }
option("s", "size") {
  description "Use N as size of genome, instead of total size in files"
  uint64; typestr "N"; suffix }
option("N") {
  description "Compute Nx statistic"
  uint32; typestr "x"; multiple }
option("E", "Esize") {
  description "Compute the E-size"
  off }
option("S", "sum") {
  description "Compute sum of size of all entries"
  off }
option("A", "average") {
  description "Compute average length of all entries"
  off }
option("C", "count") {
  description "Compute the number of sequences"
  off }
option("f", "from-sizes") {
  description "Read list of contig sizes instead of fasta"
  off }
option("t", "terse") {
  description "Old terse headers"
  off }
arg("file") {
  description "Input fasta file"
  c_string; multiple }