The alleleCount program primarily exists to prevent code duplication
between some other projects, specifically AscatNGS and Battenberg.
allele_counter(
hts_file,
loci_file,
ofile,
...,
odir = getwd(),
alleleCounter = NULL
)A command object.
A string of path to sample HTS file.
A string of path to loci file.
A string of path to the output file.
<dynamic dots> Additional arguments passed to alleleCounter command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote. Details see: cmd_help(alleleCounter()).
A string of path to the output directory.
A string of path to alleleCounter command.