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)