Multi-mapping reads filtering support in countNonSplicedReads

[mincej]

In the documentation from FRASER countRNAData, there is the following parameters:

...  Further parameters passed on to Rsubread::featureCounts.

However, when running with the parameters:

reads_onerun <- countRNAData(
    sampleID ="sample1",
    fds = fds, 
    NcpuPerSample = 8,
    recount = TRUE,
    keepNonStandardChromosomes = TRUE,
    genome = c("BSgenome.Hsapiens.UCSC.hg38"),
    countMultiMappingReads = FALSE
)

an error is returned:

Error in getNonSplitReadCountsForAllSamples(fds = fds, splitCountRanges = splitCountRanges,  : 
  unused arguments (sampleID = "sample1", countMultiMappingReads = TRUE)

In the nonspliced read counts function, the countMultiMappingReads parameter is hardcoded to FALSE.

FRASER/R/countRNAseqData.R

Lines 904 to 925 in ee6f279

	rsubreadCounts <- featureCounts(files=bamFile, annot.ext=anno,
	minOverlap=minAnchor*2,
	allowMultiOverlap=TRUE,
	checkFragLength=FALSE,
	minMQS=bamMapqFilter(scanBamParam(fds)),
	strandSpecific=strand,
	# activating long read mode
	isLongRead=longRead,
	# multi-mapping reads
	countMultiMappingReads=TRUE,
	# unstranded case: for counting only non spliced reads we
	# skip this information
	isPairedEnd=isPairedEnd,
	# sorting only needed for paired-end reads
	autosort=doAutosort,
	nthreads=NcpuPerSample,
	tmpDir=file.path(file_path_as_absolute(workingDir(fds)), "cache")
	)

This is different than countSplicedReads, which uses GenomicAlignment functions for counting which can use ScanBamParams and tagFilters for filtering bam files.

FRASER/R/countRNAseqData.R

Lines 534 to 537 in ee6f279

	countsList <- bplapply(chromosomes, FUN=countSplitReadsPerChromosome,
	bamFile=bamfile, pairedEnd=pairedend, genome=genome,
	strandMode=strandmode, scanBamParam=scanbamparam,
	BPPARAM=getBPParam(NcpuPerSample, length(chromosomes)))

FRASER/R/countRNAseqData.R

Lines 567 to 569 in ee6f279

	galignment <- readGAlignmentPairs(
	bamFile, param=param, strandMode=strandMode)
	}

FRASER/R/countRNAseqData.R

Lines 613 to 614 in ee6f279

	jc <- summarizeJunctions(galignment, genome=genome,
	with.revmap=(as.logical(strandMode) && pairedEnd) )

What is the reason that you cannot alter the multimapping count parameters for nonspliced reads, but can for spliced reads? Or am I misunderstanding how these functions work in tandem, and that the filtering for multimapping reads is done by extension when defining the spliced ranges resulting from countSplicedReads and needed as input for countNonSplicedReads?