R/RcppExports.R

In Rfastp: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

runFastp <- function(read1 = "", read2 = "", outputFastq = "", unpaired = "", failedOut = "", merge = FALSE, mergeOut = "", phred64 = FALSE, interleaved = FALSE, fixMGIid = FALSE, adapterTrimming = TRUE, adapterSequenceRead1 = "auto", adapterSequenceRead2 = "auto", adapterFasta = "", trimFrontRead1 = 0L, trimTailRead1 = 0L, trimFrontRead2 = 0L, trimTailRead2 = 0L, maxLengthRead1 = 0L, maxLengthRead2 = 0L, forceTrimPolyG = FALSE, disableTrimPolyG = FALSE, minLengthPolyG = 10L, trimPolyX = FALSE, minLengthPolyX = 10L, cutLowQualFront = FALSE, cutLowQualTail = FALSE, cutSlideWindowRight = FALSE, cutWindowSize = 4L, cutMeanQual = 20L, cutFrontWindowSize = 4L, cutFrontMeanQual = 20L, cutTailWindowSize = 4L, cutTailMeanQual = 20L, cutSlideWindowSize = 4L, cutSlideWindowQual = 20L, qualityFiltering = TRUE, qualityFilterPhred = 15L, qualityFilterPercent = 40L, maxNfilter = 5L, averageQualFilter = 0L, lengthFiltering = TRUE, minReadLength = 15L, maxReadLength = 0L, lowComplexityFiltering = FALSE, minComplexity = 30L, index1Filter = "", index2Filter = "", maxIndexMismatch = 0L, correctionOverlap = FALSE, minOverlapLength = 30L, maxOverlapMismatch = 5L, maxOverlapMismatchPercentage = 20L, umi = FALSE, umiIgnoreSeqNameSpace = FALSE, umiLoc = "", umiLength = 0L, umiPrefix = "", umiSkipBaseLength = 0L, overrepresentationAnalysis = FALSE, overrepresentationSampling = 20L, splitOutput = 0L, splitByLines = 0L, thread = 2L, verbose = TRUE) {
    .Call(`_Rfastp_runFastp`, read1, read2, outputFastq, unpaired, failedOut, merge, mergeOut, phred64, interleaved, fixMGIid, adapterTrimming, adapterSequenceRead1, adapterSequenceRead2, adapterFasta, trimFrontRead1, trimTailRead1, trimFrontRead2, trimTailRead2, maxLengthRead1, maxLengthRead2, forceTrimPolyG, disableTrimPolyG, minLengthPolyG, trimPolyX, minLengthPolyX, cutLowQualFront, cutLowQualTail, cutSlideWindowRight, cutWindowSize, cutMeanQual, cutFrontWindowSize, cutFrontMeanQual, cutTailWindowSize, cutTailMeanQual, cutSlideWindowSize, cutSlideWindowQual, qualityFiltering, qualityFilterPhred, qualityFilterPercent, maxNfilter, averageQualFilter, lengthFiltering, minReadLength, maxReadLength, lowComplexityFiltering, minComplexity, index1Filter, index2Filter, maxIndexMismatch, correctionOverlap, minOverlapLength, maxOverlapMismatch, maxOverlapMismatchPercentage, umi, umiIgnoreSeqNameSpace, umiLoc, umiLength, umiPrefix, umiSkipBaseLength, overrepresentationAnalysis, overrepresentationSampling, splitOutput, splitByLines, thread, verbose)
}

rcat <- function(output = "", inputFiles = as.character( c()), numInFile = 0L) {
    .Call(`_Rfastp_rcat`, output, inputFiles, numInFile)
}