#' generate wiggle tracks for HMMcopy
#'
#' @param sampleID the bam files
#' @param projName the project
#' @param location of bam files
#'
#' @export
genCNVwigs <- function(sampleID,projName,bamDir,bamExt="_dedup_realn_recal.bam",
outDir=file.path("/scratch/pschofield/Projects",projName,"Analysis/wigs"),
noSub=T,ncores=1,scpIt=T,mem="16Gb",windowSize,
chrNames=c(seq(1,22),"X","Y"),
hmmCopyMod= "apps/hmmcopy/0.99.0/gcc-4.4.7"){
outFile <- file.path(outDir,paste0(sampleID,"_w",windowSize,".wig"))
alignBAM <- file.path(bamDir, paste0(sampleID, bamExt))
script <- c(
paste0("mkdir -p ",outDir),
paste0("module load ",hmmCopyMod),
paste0("readCounter -w ",windowSize," -c ",paste0(chrNames,collapse=",")," ",
alignBAM," -b "),
paste0("readCounter -w ",windowSize," -c ",paste0(chrNames,collapse=",")," ",
alignBAM," > ",outFile)
)
plib::runScript(jname=paste0("genwig_",sampleID),jproj=projName,
jdesc=paste0("generate HMMCopy wig for ",projName," on sample ", sampleID),
jscrp=script,noSub=noSub,nproc=ncores,scpIt=scpIt,mem="32Gb")
}
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