Wrapper function for ctk's parseAlignment

ctk_parseAlignment(
  filesToRun,
  outFile = paste0(file_path_sans_ext(filesToRun), ".bed"),
  sb = "parseAlignment.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  mutationFile = NULL,
  mapQual = NULL,
  minLen = NULL,
  indelToEnd = 5,
  splitDel = FALSE,
  indelInScore = FALSE,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_parseAlignment_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_parseAlignment_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 (SAM).
outFile: path to output file (BED).
sb: path to parseAlignment.pl from CTK.
perl: path to PERL.
PATHTOPERLLIB: path to PERL5LIB.
mutationFile: mutation file path, default is NULL.
mapQual: minimum map quality, default is NULL.
minLen: minimum length of read, default is NULL.
indelToEnd: minimum distance from indel to end of read, default is 5.
splitDel: whether to split reads with deletions, TRUE or FALSE (default).
indelInScore: include indels in mutation score count, TRUE or FALSE (default).
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 BED file.

Author

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))
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 
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose=TRUE)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl  /Users/runner/work/_temp/Library/CLIPflexR/extdata/QT_FF_Fox3_Std_small_clip.fq  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Collapsed_QT_FF_Fox3_Std_small_clip.fq 
FqFile_QFColStripped <- ctk_stripBarcode(FqFile_Col,linkerlength=5,inputFormat="fastq")
bam <- suppressWarnings(bowtie_align(FqFile_QFColStripped,myIndex, 
overwrite=TRUE, inputFormat="fastq"))
parsedAlignment <- ctk_parseAlignment(bam)