sort_cmdline.yaggo

purpose "Sort fasta file according to header"

option("n", "numeric-sort") {
  description "Compare according to string numerical value"
  off }
option("R", "random-sort") {
  description "Random order"
  off; conflict "numeric-sort" }
option("f", "ignore-case") {
  description "Case insensitive sorting"
  off; conflict "random-sort", "numeric-sort" }
option("C", "character") {
  description "Starting character of sorting key"
  uint32; default 1 }
option("H", "header-full") {
  description "Use full line of header as sorting key, not first word"
  off }
option("k", "key") {
  description "1-index of column in header to sort by"
  uint32; default 1 }
option("write-seed") {
  description "Write seed used by random order to PATH"
  c_string; typestr "PATH" }
option("read-seed") {
  description "Read seed for random order from PATH"
  c_string; typestr "PATH" }
arg("file") {
  description "Input fasta files"
  c_string; typestr "path"; multiple }