extract_cmdline.yaggo

description "Match a header and output the content."

option("v", "--invert-match") {
  description "Invert the sense of matching, to select non-matching headers"
  off }
option("n", "name") {
  description "Extract read with NAME, exact match"
  string; multiple; typestr "NAME" }
option("f", "name-file") {
  description "File of read names to extract"
  c_string; multiple; typestr "path" }
option("p", "probabilistic") {
  description "Select sequences with probability PROBA"
  double; typestr "PROBA" }
option("m", "max-count") {
  description "Stop reading after NUM matching headers"
  uint64; typestr "NUM" }
option("s", "start") {
  description "Output content starting at byte NUM, 0-based"
  uint64; typestr "NUM" }
option("e", "end") {
  description "Output content up to byte NUM"
  uint64; typestr "NUM" }
arg("file") {
  description "Fasta files"
  c_string; multiple }