Map reads through the minibwa CLI
Usage
minibwa_map(
index,
reads,
output = NULL,
format = c("sam", "paf"),
threads = NULL,
meth = FALSE,
hic = FALSE,
extra_args = character(),
path = minibwa_path()
)Arguments
- index
Index prefix produced by
minibwa_index()or the minibwa CLI.- reads
One or more FASTA/FASTQ input paths. The common cases are one single-end file or two paired-end files.
- output
Optional output file. When
NULL, standard output is captured and returned as a character vector.- format
Output format:
"sam"by default, or"paf"to pass-f.- threads
Optional number of worker threads.
- meth
If
TRUE, pass--meth.- hic
If
TRUE, pass--hic.- extra_args
Additional CLI arguments inserted before positional arguments.
- path
Executable name or path.