Accepts a single-record GenBank file (first non-blank line starts with LOCUS) or a single-record FASTA. Unlike the custom assembly database parser, no organelle qualifier is required.
Usage
maptoref_prepare_ref(
ref_file,
topology = NA_character_,
genetic_code = NA_integer_,
out_dir = "."
)Arguments
- ref_file
Path to the reference file.
- topology
"circular" or "linear". Required for a FASTA reference. For GenBank, the LOCUS line wins when it states one; otherwise this value is used and is required.
- genetic_code
The sample's genetic code, used only to warn when the reference disagrees.
- out_dir
Directory to write the `maptoref/` working files into.