Wrapper function for ctk's fastq_filter

ctk_fastqFilter(
  filesToRun,
  outFile = file.path(dirname(fileToRun), paste("FF_", basename(fileToRun), sep = "")),
  sb = "fastq_filter.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  fastqFormat = "sanger",
  indexPosition = NULL,
  qsFilter = NULL,
  maxN = NULL,
  outputFormat = "fastq",
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_fastqFilter_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_fastqFilter_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

filesToRun: path to file to process (fastq).
outFile: output file (fastq).
sb: path to fastq_filter.pl from CTK.
perl: path to PERL.
PATHTOPERLLIB: path to PERL5LIB.
fastqFormat: fastq format used, can be "sanger" (default) or "solexa".
indexPosition: position and sequence of index in read, default is NULL; set "position:seqeunce" to specify (e.g. "1:CATCGC").
qsFilter: set quality score filter, default is NULL; set method:start-end:score to specify (e.g. "mean:0-29:20"; starts/ends are 0-based).
maxN: maximum number of unknown nucleotides (N) allowed, default is NULL; set to integer to specify.
outputFormat: output format, "fastq" (default) or "fasta".
stderr: path to stdout 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, TRUE or FALSE (default).
writelog: write stderr/stdout logs, TRUE (default) or FALSE.

Value

Path to filtered file in specified format.

Author

Kathryn Rozen-Gagnon

Examples

testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter = "mean:0-29:20",verbose=TRUE)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl  -if sanger  -of fastq  -f mean:0-29:20  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Fox3_Std_small.fq.gz  /Users/runner/work/_temp/Library/CLIPflexR/extdata/FF_Fox3_Std_small.fq.gz