Nothing
interestAnalyse.sequential <-
function(
reference,
bamFile,
isPaired,
yieldSize,
maxNoMappedReads,
logFile,
method,
appendLogFile=TRUE,
repeatsTableToFilter,
referenceIntronExon,
junctionReadsOnly,
isPairedDuplicate,
isSingleReadDuplicate,
...)
{
resTmpPair<-c()
resTmpSingle<- c()
#Paralle running impelementation
if(logFile!=""){
cat( "InERESt:interestAnalyse: Begins ...\n", file=logFile,
append=appendLogFile)
}
cat( "InERESt:interestAnalyse: Begins ...\n")
if(is(reference,"GRanges")){
if(length(names(reference))>0){
tmpReference=data.frame(
chr=as.character(GenomicRanges::seqnames(reference)),
begin=as.numeric(GenomicRanges::start(reference)),
end=as.numeric(GenomicRanges::end(reference)),
strand=as.character(GenomicRanges::strand(reference)),
names=as.character(names(reference)))
} else{
tmpReference=data.frame(
chr=as.character(GenomicRanges::seqnames(reference)),
begin=as.numeric(GenomicRanges::start(reference)),
end=GenomicRanges::end(reference),
strand=as.character(GenomicRanges::strand(reference)))
}
reference=tmpReference
}
time1=Sys.time()
# Set parallel environment
bpparam <- BiocParallel::SerialParam()
# Initialize the iterator and combine with REDUCE:
if(isPaired){
#Defining connecting to bam file
bf<- Rsamtools::BamFile(bamFile, yieldSize=yieldSize,
asMates=TRUE, ...)
# Analyzing mapped paired reads together
scParam=Rsamtools::ScanBamParam(
what=Rsamtools::scanBamWhat()[c(1,
3,5,8,13,9, 10, 6, 4, 14, 15)],
flag=Rsamtools::scanBamFlag(isPaired=TRUE,
isDuplicate=isPairedDuplicate))
ITER <- bamIterPair(bf, scParam= scParam)
resTmpPair<- BiocParallel::bpiterate(ITER, interestIntExAnalysePair,
reference=reference,
maxNoMappedReads=maxNoMappedReads,
logFile=logFile,
method=method,
appendLogFile=appendLogFile,
repeatsTableToFilter=repeatsTableToFilter,
referenceIntronExon=referenceIntronExon,
junctionReadsOnly=junctionReadsOnly,
BPPARAM=bpparam)
# Analyzing single mapped reads
scParam=Rsamtools::ScanBamParam(
what=Rsamtools::scanBamWhat()[c(1,
3,5,8,13,9, 10, 6, 4, 14, 15)],
flag=Rsamtools::scanBamFlag(hasUnmappedMate=TRUE,
isPaired=TRUE,
isDuplicate=isSingleReadDuplicate))
ITER <- bamIterSingle(bf, scParam= scParam)
resTmpSingle<- BiocParallel::bpiterate(ITER,
interestIntExAnalyseSingle,
reference=reference,
maxNoMappedReads=maxNoMappedReads,
logFile=logFile,
method=method,
appendLogFile=appendLogFile,
repeatsTableToFilter=repeatsTableToFilter,
referenceIntronExon=referenceIntronExon,
junctionReadsOnly=junctionReadsOnly,
BPPARAM=bpparam)
} else {
#Defining connecting to bam file
bf<- Rsamtools::BamFile(bamFile, yieldSize=yieldSize, ...)
#Analyzing unpaired sequencing data
scParam=Rsamtools::ScanBamParam(
what=Rsamtools::scanBamWhat()[c(1,
3,5,8,13,9, 10, 6, 4, 14, 15)],
flag=Rsamtools::scanBamFlag(
isPaired=NA,
isDuplicate=isSingleReadDuplicate))
ITER <- bamIterSingle(bf, scParam= scParam)
resTmpSingle<- BiocParallel::bpiterate(ITER,
interestIntExAnalyseSingle,
reference=reference,
maxNoMappedReads=maxNoMappedReads,
logFile=logFile,
method=method,
appendLogFile=appendLogFile,
repeatsTableToFilter=repeatsTableToFilter,
referenceIntronExon=referenceIntronExon,
junctionReadsOnly=junctionReadsOnly,
BPPARAM=bpparam)
}
resPair<-rep(0, nrow(reference)*length(method))
resSingle<-rep(0, nrow(reference)*length(method))
if(isPaired & (length(resTmpPair)>0)){
resTmpPair[sapply(resTmpPair, is.null)] <- NULL
resPair<-Reduce("+", resTmpPair)
}
if(length(resTmpSingle)>0){
resTmpSingle[sapply(resTmpSingle, is.null)] <- NULL
resSingle<-Reduce("+", resTmpSingle)
}
res<- resPair+resSingle
time2=Sys.time()
runTime=difftime(time2,time1, units="secs")
if(logFile!="")
cat( "InERESt:interestAnalyse: Read counting ends. Running time: ",
runTime," secs\n", file=logFile, append=TRUE)
cat( "InERESt:interestAnalyse: Read counting ends. Running time: ",
runTime," secs\n")
return(res)
}
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