Wrapper function for fastx_barcode_splitter — fastx_barcode

Split multiplexed samples by user-defined indics using fastx_barcode_splitter

fastx_barcode_splitter(
  fileTofxc,
  bcFile,
  mismatches = 0,
  fbs = "fastx_barcode_splitter.pl",
  stderr = file.path(dirname(fileTofxc), paste0(basename(fileTofxc),
    "_fastx_barcode_splitter_stderr.txt")),
  stdout = file.path(dirname(fileTofxc), paste0(basename(fileTofxc),
    "_fastx_barcode_splitter_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE
)

Arguments

fileTofxc: path to file to process (fastq or fasta).
bcFile: tab-delimited barcode file.
mismatches: number of mismatches allowed.
fbs: path to fastx_barcode_splitter.pl from FASTX toolkit.
stderr: path to stderr file.
stdout: path to stdout file.
useClipRConda: use conda environment installed by Herper, TRUE (default) or FALSE.
additional_Args: additional arguments to be passed to system call.
verbose: print messages to screen, TRUE or FALSE (default).

Value

path to split files; files will be written without any extension, in the same format as the input file.

Author

Kathryn Rozen-Gagnon