Native minibwa options

Returns a plain list consumed by native mapping functions. Only the selected options are exposed initially; all other fields use minibwa defaults for the chosen preset.

Usage

mb_opts(
  preset = c("adap", "sr", "lr"),
  paired = NULL,
  methylation = NULL,
  out_n = NULL,
  min_seed_len = NULL,
  threads = NULL,
  match_score = NULL,
  mismatch_penalty = NULL,
  gap_open = NULL,
  gap_extend = NULL
)

Arguments

preset

One of "adap", "sr", or "lr".

paired, methylation

Optional logical overrides for minibwa flags.

out_n, min_seed_len, threads, match_score, mismatch_penalty, gap_open, gap_extend

Optional integer overrides for common minibwa fields.

Value

A plain list.