Assigns a MapToRef reference mitogenome to individual samples in an existing project. A reference has one home, the sample row; the parameter set the sample is on supplies the mapper and its options. A FASTA reference also needs a topology (circular or linear) in the third column. A blank reference clears both values.
Arguments
- path
Path to the project directory (default = current working directory)
- refs
A CSV path or a data frame. The first column holds sample IDs and the second holds references; column names are ignored, but a CSV must have a header row (its first line is not read as data). An optional third column holds the topology, required for a FASTA reference; any further columns are ignored. A reference is an absolute file path to a single-record GenBank or FASTA mitogenome, a URL, or an NCBI nucleotide accession (for example NC_002333). Blank clears the sample's reference.