fastq2otu: FASTQ2OTU: Automate microbiome analyses

Documented in readConfig

#' Read in a config file (preferred method)
#'
#' This function parses config file to extract data needed to create a FASTQ2OTU class object. It assumes that
#' the file is in YML format and contains default key terms.
#' Execute getSlots("fastq2otu") to get all required arguments or refer to documenation for more details and/or
#' examples.
#'
#' Use when config file is supplied and all required values are provided.
#' @param configFile Path to config file (YML-formatted)
#' @param isPaired Default is FALSE. If TRUE, parameters for paired-end data will be used. 
#' @param type Default is 'auto'. String or vector containing the following value(s): 'auto', 'assignTax', 'report', 'seqdump', 'primertrim', 'filter', 'qualityplot'. Used to specify what type of object is being created.
#' If a vector is provided it must contain one of the following combination of strings c('auto', 'assignTax') and  c('auto', 'filter')
#' @return An S4 object
#' @importFrom yaml yaml.load_file
#' @export
readConfig <- function(configFile, isPaired = FALSE, type = c('auto')) {
	
	if (!file.exists(configFile)) {
			stop(sprintf("%s could not be found, please enter a valid path", configFile))
	}
	options <- yaml::yaml.load_file(configFile)

	# Check to see if a valid type is provided
	key <- c('auto', 'assignTax', 'report', 'seqdump', 'primertrim', 'filter', 'qualityplot')
	if (all(type %in% key)) {
		# Do Nothing (returns NULL)		
	} else {
		stop("Invalid parameter. Could not identify type.")
	}

	# Create new fastq2otu class object based on sequencing method
	if ("assignTax" %in% type & isPaired) {
		if (length(type) == 1) {
			mytemp <- setFastAssignTaxa(refDatabase = options$taxDatabase, 
					prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
					minBootstrap = `if`(!is.null(options$assignTaxMinBootstrap), options$assignTaxMinBootstrap, 50), 
					tryComplement = `if`(!is.null(options$assignTaxTryComplement), options$assignTaxTryComplement, FALSE), 
					showBootstraps = `if`(!is.null(options$assignTaxOutputBootstraps), options$assignTaxOutputBootstraps, FALSE), 
					taxLevels = `if`(!is.null(options$assignTaxLevels), as.vector(options$assignTaxLevels), c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")),
					verbose = `if`(!is.null(options$verbose), options$verbose, FALSE), 
					multithread = `if`(!is.null(options$multithread), options$multithread, FALSE))
		} 
		else if ('auto' %in% type & length(type) == 2) {
			mytemp <- setFastAssignTaxa(refDatabase = options$taxDatabase,
                                        prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
                                        minBootstrap = `if`(!is.null(options$assignTaxMinBootstrap), options$assignTaxMinBootstrap, 50),
                                        tryComplement = `if`(!is.null(options$assignTaxTryComplement), options$assignTaxTryComplement, FALSE),
                                        showBootstraps = `if`(!is.null(options$assignTaxOutputBootstraps), options$assignTaxOutputBootstraps, FALSE),
                                        taxLevels = `if`(!is.null(options$assignTaxLevels), as.vector(options$assignTaxLevels), c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")),
                                        verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
                                        multithread = `if`(!is.null(options$multithread), options$multithread, FALSE))
			
			mytemp@inDir <- options$pathToData
			mytemp@outDir <- options$outDir 
			mytemp@doMergeSeqPairs <- `if`(!is.null(options$mergePairs), options$mergePairs, FALSE) 
			mytemp@mergeSeqPairsTrimOverhang <- `if`(!is.null(options$mergePairsTrimOverhang), options$mergePairsTrimOverhang, FALSE)
			mytemp@mergeSeqPairsMinOverlap <- `if`(!is.null(options$mergePairsMinOverlap), options$mergePairsMinOverlap, 12)
			mytemp@mergeSeqPairsMaxMismatch <- `if`(!is.null(options$mergePairsMaxMismatch), options$mergePairsMaxMismatch, 0)
			mytemp@mergeSeqPairsReturnRejects <- `if`(!is.null(options$mergePairsReturnRejects), options$mergePairsReturnRejects, FALSE)
			mytemp@mergeSeqPairsJustConcatenate <- `if`(!is.null(options$mergePairsJustConcatenate), options$mergePairsJustConcatenate, FALSE)
			mytemp@isPaired <- TRUE
			mytemp@derepN <- `if`(!is.null(options$derepN), as.numeric(as.character(options$derepN)), 1e+06)
			mytemp@saveErrorsPlotPDF <- `if`(!is.null(options$saveErrorsPlot), options$saveErrorsPlot, FALSE)
			mytemp@errN <- `if`(!is.null(options$errN), as.numeric(as.character(options$errN)), 1e+08)
			mytemp@dadaBandSize <- `if`(!is.null(options$dadaBandSize), as.numeric(as.character(options$dadaBandSize)), 16) 
			mytemp@dadaOmegaA <- `if`(!is.null(options$dadaOmegaA), as.numeric(as.character(options$dadaOmegaA)), 1e-40)
			mytemp@createChimeraDetectionTable <- `if`(!is.null(options$createChimeraDetectionTable), options$createChimeraDetectionTable, FALSE)
			mytemp@chimeraDetectionMinSampleFraction <- `if`(!is.null(options$chimeraDetectionMinSampleFraction), as.numeric(as.character(options$chimeraDetectionMinSampleFraction)), 0.9) 
			mytemp@chimeraDetectionIgnoreNegatives <- `if`(!is.null(options$chimeraDetectionIgnoreNegatives), as.numeric(as.character(options$chimeraDetectionIgnoreNegatives)), 1)
			mytemp@chimeraDetectionMinFoldParentOverAbundance <- `if`(!is.null(options$chimeraDetectionMinFoldParentOverabundance), as.numeric(as.character(options$chimeraDetectionMinFoldParentOverabundance)), 1.5) 
			mytemp@chimeraDetectionParentAbundance <- `if`(!is.null(options$chimeraDetectionParentAbundance), as.numeric(as.character(options$chimeraDetectionParentAbundance)), 2) 
			mytemp@chimeraDetectionAllowOneOff <- `if`(!is.null(options$chimeraDetectionAllowOneOff), options$chimeraDetectionAllowOneOff, FALSE)
			mytemp@chimeraDetectionMaxShift <- `if`(!is.null(options$chimeraDetectionMaxShift), as.numeric(as.character(options$chimeraDetectionMaxShift)), 16)
		}
		else {
			stop("Invalid type input(s) provided")
		}
	}
	else if ("filter" %in% type & isPaired) {
		if (length(type) == 1) {
			mytemp <- setFastFilter(inDir = options$pathToData,
					outDir = options$outDir,
					verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
					prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"), 
					maxEE = `if`(!is.null(options$filtMaxEE), as.numeric(as.character(options$filtMaxEE)), c(2.5, 2.5)), 
					truncQ = `if`(!is.null(options$filtTruncQ), as.numeric(as.character(options$filtTruncQ)), c(0, 0)), 
					truncLen = `if`(!is.null(options$filtTruncLen), as.numeric(as.character(options$filtTruncLen)), c(0, 0)), 
					trimLeft = `if`(!is.null(options$filtTrimLeft), as.numeric(as.character(options$filtTrimLeft)), c(0, 0)),
					trimRight = `if`(!is.null(options$filtTrimRight), as.numeric(as.character(options$filtTrimRight)), c(0, 0)), 
					matchIDs = `if`(!is.null(options$filtMatchIDs), options$filtMatchIDs, FALSE), 
					minLen = `if`(!is.null(options$filtMinLen), as.numeric(as.character(options$filtMinLen)), c(50, 50)),
					isPaired = TRUE, 
					multithread = `if`(!is.null(options$multithread), options$multithread, FALSE)) 
		}
		else if ("auto" %in% type & length(type) == 2) { 
			mytemp <- setFastFilter(inDir = options$pathToData,
                                        outDir = options$outDir,
                                        verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
                                        prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
                                        maxEE = `if`(!is.null(options$filtMaxEE), as.numeric(as.character(options$filtMaxEE)), c(2.5, 2.5)),
                                        truncQ = `if`(!is.null(options$filtTruncQ), as.numeric(as.character(options$filtTruncQ)), c(0, 0)),
                                        truncLen = `if`(!is.null(options$filtTruncLen), as.numeric(as.character(options$filtTruncLen)), c(0, 0)),
                                        trimLeft = `if`(!is.null(options$filtTrimLeft), as.numeric(as.character(options$filtTrimLeft)), c(0, 0)),
                                        trimRight = `if`(!is.null(options$filtTrimRight), as.numeric(as.character(options$filtTrimRight)), c(0, 0)),
                                        matchIDs = `if`(!is.null(options$filtMatchIDs), options$filtMatchIDs, FALSE),
                                        minLen = `if`(!is.null(options$filtMinLen), as.numeric(as.character(options$filtMinLen)), c(50, 50)),
                                        isPaired = TRUE,
                                        multithread = `if`(!is.null(options$multithread), options$multithread, FALSE))


			
			mytemp@chimeraDetectionAllowOneOff <- `if`(!is.null(options$chimeraDetectionAllowOneOff), options$chimeraDetectionAllowOneOff, FALSE) 
			mytemp@dadaBandSize <- `if`(!is.null(options$dadaBandSize), as.numeric(as.character(options$dadaBandSize)), 16) 
			mytemp@dadaOmegaA <- `if`(!is.null(options$dadaOmegaA), as.numeric(as.character(options$dadaOmegaA)), 1e-40) 
			mytemp@derepN <- `if`(!is.null(options$derepN), as.numeric(as.character(options$derepN)), 1e+06)
			mytemp@chimeraDetectionParentAbundance <- `if`(!is.null(options$chimeraDetectionParentAbundance), as.numeric(as.character(options$chimeraDetectionParentAbundance)), 2) 
			mytemp@errN <- `if`(!is.null(options$errN), as.numeric(as.character(options$errN)), 1e+08)
			mytemp@createChimeraDetectionTable <- `if`(!is.null(options$createChimeraDetectionTable), options$createChimeraDetectionTable, FALSE) 
			mytemp@saveErrorsPlotPDF <- `if`(!is.null(options$saveErrorsPlot), options$saveErrorsPlot, FALSE)
			mytemp@chimeraDetectionIgnoreNegatives <- `if`(!is.null(options$chimeraDetectionIgnoreNegatives), as.numeric(as.character(options$chimeraDetectionIgnoreNegatives)), 1) 
			mytemp@mergeSeqPairsJustConcatenate <- `if`(!is.null(options$mergePairsJustConcatenate), options$mergePairsJustConcatenate, FALSE)
			mytemp@mergeSeqPairsMaxMismatch <- `if`(!is.null(options$mergePairsMaxMismatch), as.numeric(as.character(options$mergePairsMaxMismatch)), 0)
			mytemp@chimeraDetectionMaxShift <- `if`(!is.null(options$chimeraDetectionMaxShift), as.numeric(as.character(options$chimeraDetectionMaxShift)), 16)
			mytemp@doMergeSeqPairs <- `if`(!is.null(options$mergePairs), options$mergePairs, FALSE)
			mytemp@chimeraDetectionMinFoldParentOverabundance = `if`(!is.null(options$chimeraDetectionMinFoldParentOverabundance), as.numeric(as.character(options$chimeraDetectionMinFoldParentOverabundance)), 1.5) 
			mytemp@mergeSeqPairsMinOverlap <- `if`(!is.null(options$mergePairsMinOverlap), as.numeric(as.character(options$mergePairsMinOverlap)), 12)
			mytemp@chimeraDetectionMinSampleFraction <- `if`(!is.null(options$chimeraDetectionMinSampleFraction), as.numeric(as.character(options$chimeraDetectionMinSampleFraction)), 0.9) 
			mytemp@mergeSeqPairsReturnRejects <- `if`(!is.null(options$mergePairsReturnRejects), options$mergePairsReturnRejects,FALSE)
 			mytemp@mergeSeqPairsTrimOverhang <- `if`(!is.null(options$mergePairsTrimOverhang), options$mergePairsTrimOverhang, FALSE)
		}
		else {
			stop("Invalid type input(s) provided")
		}
	}
	else if (all("auto" == type) & isPaired) {
		# fastPaired object is created
		mytemp <- setFastPaired(inDir = options$pathToData,
							outDir = options$outDir, 
							mergeSeqs = `if`(!is.null(options$mergePairs), options$mergePairs, FALSE), 
							trimOverhang = `if`(!is.null(options$mergePairsTrimOverhang), options$mergePairsTrimOverhang, FALSE),
							minOverlap = `if`(!is.null(options$mergePairsMinOverlap), as.numeric(as.character(options$mergePairsMinOverlap)), 12),
							maxMismatch = `if`(!is.null(options$mergePairsMaxMismatch), as.numeric(as.character(options$mergePairsMaxMismatch)), 0), 
							returnRejects = `if`(!is.null(options$mergePairsReturnRejects), options$mergePairsReturnRejects, FALSE), 
							justConcatenate = `if`(!is.null(options$mergePairsJustConcatenate), options$mergePairsJustConcatenate, FALSE),
							verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
							prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
							isPaired = TRUE, 
							derepN = `if`(!is.null(options$derepN), as.numeric(as.character(options$derepN)), 1e+06),
							getErrPDF = `if`(!is.null(options$saveErrorsPlot), options$saveErrorsPlot, FALSE),
							errN = `if`(!is.null(options$errN), as.numeric(as.character(options$errN)), 1e+08), 
							multithread = `if`(!is.null(options$multithread), options$multithread, FALSE),
							dadaBandSize = `if`(!is.null(options$dadaBandSize), as.numeric(as.character(options$dadaBandSize)), 16), 
							dadaOmegaA = `if`(!is.null(options$dadaOmegaA), as.numeric(as.character(options$dadaOmegaA)), 1e-40), 
							getChimeraTable = `if`(!is.null(options$createChimeraDetectionTable), options$createChimeraDetectionTable, FALSE), 
							minSampleFraction = `if`(!is.null(options$chimeraDetectionMinSampleFraction), options$chimeraDetectionMinSampleFraction, 0.9), 
							ignoreNegatives = `if`(!is.null(options$chimeraDetectionIgnoreNegatives), as.numeric(as.character(options$chimeraDetectionIgnoreNegatives)), 1), 
							minFoldParentOverAbundance = `if`(!is.null(options$chimeraDetectionMinFoldParentOverabundance), as.numeric(as.character(options$chimeraDetectionMinFoldParentOverabundance)), 1.5), 
							detectionAbundance = `if`(!is.null(options$chimeraDetectionParentAbundance), as.numeric(as.character(options$chimeraDetectionParentAbundance)), 2), 
							allowOneOff = `if`(!is.null(options$chimeraDetectionAllowOneOff), options$chimeraDetectionAllowOneOff, FALSE), 
							maxShift = `if`(!is.null(options$chimeraDetectionMaxShift), as.numeric(as.character(options$chimeraDetectionMaxShift)), 16))
	}
	else if (all("auto" == type) & !isPaired) {
		mytemp <- setFastSingle(inDir = options$pathToData,
							outDir = options$outDir, 
							verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
							prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
							isPaired = FALSE, 
							derepN = `if`(!is.null(options$derepN), as.numeric(as.character(options$derepN)), 1e+06),
							getErrPDF = `if`(!is.null(options$saveErrorsPlot), options$saveErrorsPlot, FALSE),
							errN = `if`(!is.null(options$errN), as.numeric(as.character(options$errN)), 1e+08), 
							multithread = `if`(!is.null(options$multithread), options$multithread, FALSE),
							dadaBandSize = `if`(!is.null(options$dadaBandSize), as.numeric(as.character(options$dadaBandSize)), 16), 
							dadaOmegaA = `if`(!is.null(options$dadaOmegaA), as.numeric(as.character(options$dadaOmegaA)), 1e-40), 
							getChimeraTable = `if`(!is.null(options$createChimeraDetectionTable), options$createChimeraDetectionTable, FALSE), 
							minSampleFraction = `if`(!is.null(options$chimeraDetectionMinSampleFraction), as.numeric(as.character(options$chimeraDetectionMinSampleFraction)), 0.9), 
							ignoreNegatives = `if`(!is.null(options$chimeraDetectionIgnoreNegatives), as.numeric(as.character(options$chimeraDetectionIgnoreNegatives)), 1), 
							minFoldParentOverAbundance = `if`(!is.null(options$chimeraDetectionMinFoldParentOverabundance), as.numeric(as.character(options$chimeraDetectionMinFoldParentOverabundance)), 1.5), 
							detectionAbundance = `if`(!is.null(options$chimeraDetectionParentAbundance), as.numeric(as.character(options$chimeraDetectionParentAbundance)), 2), 
							allowOneOff = `if`(!is.null(options$chimeraDetectionAllowOneOff), options$chimeraDetectionAllowOneOff, FALSE), 
							maxShift = `if`(!is.null(options$chimeraDetectionMaxShift), as.numeric(as.character(options$chimeraDetectionMaxShift)), 16))
	}
	else if ("assignTax" %in% type & !isPaired) {
		if (length(type) == 1) {
			mytemp <- setFastAssignTaxa(refDatabase = options$taxDatabase, 
						prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
						minBootstrap = `if`(!is.null(options$assignTaxMinBootstrap), as.numeric(as.character(options$assignTaxMinBootstrap)), 50), 
						tryComplement = `if`(!is.null(options$assignTaxTryComplement), options$assignTaxTryComplement, FALSE), 
						showBootstraps = `if`(!is.null(options$assignTaxOutputBootstraps), options$assignTaxOutputBootstraps, FALSE), 
						taxLevels = `if`(!is.null(options$assignTaxLevels), as.vector(options$assignTaxLevels), c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")),
						verbose = `if`(!is.null(options$verbose), options$verbose, FALSE), 
						multithread = `if`(!is.null(options$multithread), options$multithread, FALSE))
		}
		else if ("auto" %in% type & length(type) == 2) {
			mytemp <- setFastAssignTaxa(refDatabase = options$taxDatabase,
                                                prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
                                                minBootstrap = `if`(!is.null(options$assignTaxMinBootstrap), as.numeric(as.character(options$assignTaxMinBootstrap)), 50),
                                                tryComplement = `if`(!is.null(options$assignTaxTryComplement), options$assignTaxTryComplement, FALSE),
                                                showBootstraps = `if`(!is.null(options$assignTaxOutputBootstraps), options$assignTaxOutputBootstraps, FALSE),
                                                taxLevels = `if`(!is.null(options$assignTaxLevels), as.vector(options$assignTaxLevels), c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")),
                                                verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
                                                multithread = `if`(!is.null(options$multithread), options$multithread, FALSE))

		
			mytemp@inDir <- options$pathToData
                        mytemp@outDir <- options$outDir
                        mytemp@doMergeSeqPairs <- `if`(!is.null(options$mergePairs), options$mergePairs, FALSE)
                        mytemp@mergeSeqPairsTrimOverhang <- `if`(!is.null(options$mergePairsTrimOverhang), options$mergePairsTrimOverhang, FALSE)
                        mytemp@mergeSeqPairsMinOverlap <- `if`(!is.null(options$mergePairsMinOverlap), options$mergePairsMinOverlap, 12)
                        mytemp@mergeSeqPairsMaxMismatch <- `if`(!is.null(options$mergePairsMaxMismatch), options$mergePairsMaxMismatch, 0)
                        mytemp@mergeSeqPairsReturnRejects <- `if`(!is.null(options$mergePairsReturnRejects), options$mergePairsReturnRejects, FALSE)
                        mytemp@mergeSeqPairsJustConcatenate <- `if`(!is.null(options$mergePairsJustConcatenate), options$mergePairsJustConcatenate, FALSE)
                        mytemp@isPaired <- FALSE
                        mytemp@derepN <- `if`(!is.null(options$derepN), as.numeric(as.character(options$derepN)), 1e+06)
                        mytemp@saveErrorsPlotPDF <- `if`(!is.null(options$saveErrorsPlot), options$saveErrorsPlot, FALSE)
                        mytemp@errN <- `if`(!is.null(options$errN), as.numeric(as.character(options$errN)), 1e+08)
                        mytemp@dadaBandSize <- `if`(!is.null(options$dadaBandSize), as.numeric(as.character(options$dadaBandSize)), 16)
                        mytemp@dadaOmegaA <- `if`(!is.null(options$dadaOmegaA), as.numeric(as.character(options$dadaOmegaA)), 1e-40)
                        mytemp@createChimeraDetectionTable <- `if`(!is.null(options$createChimeraDetectionTable), options$createChimeraDetectionTable, FALSE)
                        mytemp@chimeraDetectionMinSampleFraction <- `if`(!is.null(options$chimeraDetectionMinSampleFraction), as.numeric(as.character(options$chimeraDetectionMinSampleFraction)), 0.9)
                        mytemp@chimeraDetectionIgnoreNegatives <- `if`(!is.null(options$chimeraDetectionIgnoreNegatives), as.numeric(as.character(options$chimeraDetectionIgnoreNegatives)), 1)
                        mytemp@chimeraDetectionMinFoldParentOverabundance <- `if`(!is.null(options$chimeraDetectionMinFoldParentOverabundance), as.numeric(as.character(options$chimeraDetectionMinFoldParentOverabundance)), 1.5)
                        mytemp@chimeraDetectionParentAbundance <- `if`(!is.null(options$chimeraDetectionParentAbundance), as.numeric(as.character(options$chimeraDetectionParentAbundance)), 2)
                        mytemp@chimeraDetectionAllowOneOff <- `if`(!is.null(options$chimeraDetectionAllowOneOff), options$chimeraDetectionAllowOneOff, FALSE)
                        mytemp@chimeraDetectionMaxShift <- `if`(!is.null(options$chimeraDetectionMaxShift), as.numeric(as.character(options$chimeraDetectionMaxShift)), 16)

								
		}
		else {
			stop("Invalid input provided for type parameter")
		}				
	}
	else if ("filter" %in% type & !isPaired) {
		if (length(type) == 1) {
			mytemp <- setFastFilter(inDir = options$pathToData,
					outDir = options$outDir, 
					verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
					prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"), 
					maxEE = `if`(!is.null(options$filtMaxEE), as.numeric(as.character(options$filtMaxEE)), 2.5), 
					truncQ = `if`(!is.null(options$filtTruncQ), as.numeric(as.character(options$filtTruncQ)), 0), 
					truncLen = `if`(!is.null(options$filtTruncLen), as.numeric(as.character(options$filtTruncLen)), 0), 
					trimLeft = `if`(!is.null(options$filtTrimLeft), as.numeric(as.character(options$filtTrimLeft)), 0),
					trimRight = `if`(!is.null(options$filtTrimRight), as.numeric(as.character(options$filtTrimRight)), 0), 
					minLen = `if`(!is.null(options$filtMinLen), as.numeric(as.character(options$filtMinLen)), 50),
					isPaired = FALSE, 
					multithread = `if`(!is.null(options$multithread), options$multithread, FALSE)) 
		}		
		else if ("auto" %in% type & length(type) == 2) {
			mytemp <- setFastFilter(inDir = options$pathToData,
                                        outDir = options$outDir,
                                        verbose = `if`(!is.null(options$verbose), options$verbose, FALSE),
                                        prefix = `if`(!is.null(options$projectPrefix), options$projectPrefix, "myproject"),
                                        maxEE = `if`(!is.null(options$filtMaxEE), as.numeric(as.character(options$filtMaxEE)), 2.5),
                                        truncQ = `if`(!is.null(options$filtTruncQ), as.numeric(as.character(options$filtTruncQ)), 0),
                                        truncLen = `if`(!is.null(options$filtTruncLen), as.numeric(as.character(options$filtTruncLen)),0),
                                        trimLeft = `if`(!is.null(options$filtTrimLeft), as.numeric(as.character(options$filtTrimLeft)), 0),
                                        trimRight = `if`(!is.null(options$filtTrimRight), as.numeric(as.character(options$filtTrimRight)), 0),
                                        matchIDs = `if`(!is.null(options$filtMatchIDs), options$filtMatchIDs, FALSE),
                                        minLen = `if`(!is.null(options$filtMinLen), as.numeric(as.character(options$filtMinLen)), 50),
                                        isPaired = FALSE,
                                        multithread = `if`(!is.null(options$multithread), options$multithread, FALSE))



                        mytemp@chimeraDetectionAllowOneOff <- `if`(!is.null(options$chimeraDetectionAllowOneOff), options$chimeraDetectionAllowOneOff, FALSE)
                        mytemp@dadaBandSize <- `if`(!is.null(options$dadaBandSize), as.numeric(as.character(options$dadaBandSize)), 16)
                        mytemp@dadaOmegaA <- `if`(!is.null(options$dadaOmegaA), as.numeric(as.character(options$dadaOmegaA)), 1e-40)
                        mytemp@derepN <- `if`(!is.null(options$derepN), as.numeric(as.character(options$derepN)), 1e+06)
                        mytemp@chimeraDetectionMinFoldParentOverabundance <- `if`(!is.null(options$chimeraDetectionParentAbundance), as.numeric(as.character(options$chimeraDetectionParentAbundance)), 2)
                        mytemp@errN <- `if`(!is.null(options$errN), as.numeric(as.character(options$errN)), 1e+08)
                        mytemp@createChimeraDetectionTable <- `if`(!is.null(options$createChimeraDetectionTable), options$createChimeraDetectionTable, FALSE)
                        mytemp@saveErrorsPlotPDF <- `if`(!is.null(options$saveErrorsPlot), options$saveErrorsPlot, FALSE)
                        mytemp@chimeraDetectionIgnoreNegatives <- `if`(!is.null(options$chimeraDetectionIgnoreNegatives), as.numeric(as.character(options$chimeraDetectionIgnoreNegatives)), 1)
                        mytemp@mergeSeqPairsJustConcatenate <- `if`(!is.null(options$mergePairsJustConcatenate), options$mergePairsJustConcatenate, FALSE)
                        mytemp@mergeSeqPairsMaxMismatch <- `if`(!is.null(options$mergePairsMaxMismatch), as.numeric(as.character(options$mergePairsMaxMismatch)), 0)
                        mytemp@chimeraDetectionMaxShift <- `if`(!is.null(options$chimeraDetectionMaxShift), as.numeric(as.character(options$chimeraDetectionMaxShift)), 16)
                        mytemp@doMergeSeqPairs <- `if`(!is.null(options$mergePairs), options$mergePairs, FALSE)
                        mytemp@chimeraDetectionMinFoldParentOverabundance <- `if`(!is.null(options$chimeraDetectionMinFoldParentOverabundance), as.numeric(as.character(options$chimeraDetectionMinFoldParentOverabundance)), 1.5)
                        mytemp@mergeSeqPairsMinOverlap <- `if`(!is.null(options$mergePairsMinOverlap), as.numeric(as.character(options$mergePairsMinOverlap)), 12)
                        mytemp@chimeraDetectionMinSampleFraction <- `if`(!is.null(options$chimeraDetectionMinSampleFraction), as.numeric(as.character(options$chimeraDetectionMinSampleFraction)), 0.9)
                        mytemp@mergeSeqPairsReturnRejects <- `if`(!is.null(options$mergePairsReturnRejects), options$mergePairsReturnRejects, FALSE)
                        mytemp@mergeSeqPairsTrimOverhang <- `if`(!is.null(options$mergePairsTrimOverhang), options$mergePairsTrimOverhang, FALSE)

		}
		else {
			stop("Invalid input provided for type parameter")
		}	
	}
	else if (all("report" == type)) {
		mytemp <- setFastReport(inDir = options$pathToData,
							outDir = options$outDir, 
							fastqcPath = options$pathToFastqc, 
							installFastqc = `if`(!is.null(options$installFastqc), options$installFastqc, FALSE),
							numThreads = `if`(!is.null(options$fastqcThreads), as.numeric(as.character(options$fastqcThreads)), 4), 
							description = `if`(!is.null(options$fastqcExperimentDescription), options$fastqcExperimentDescription, "My Project"))
	}
	else if (all("seqdump" == type)) {
		mytemp <- setFastSeqDump(sampleURLs = options$pathToSampleURLs, 
							outDir = options$pathToData, 
							sampleList = options$pathToSampleIDs,
							useFastqDump = options$useFastqDump,
							fastqDumpPath = options$pathToFastqDump)
	
	}
	else if (all("primertrim" == type)) {
		mytemp <- setFastPrimerTrim(inDir = options$pathToRawFastq,
							outDir = options$pathToData,  
							adapterList = options$listOfAdapters)
	}
	else if (all("qualityplot" == type)) {
		mytemp <- setfastPlotQuality(aggregate = `if`(!is.null(options$aggregateQual), options$aggregateQual, TRUE), 
							N = `if`(!is.null(options$qualN), as.numeric(as.character(options$qualN)), 5e+05))
	}
	else { 
		stop("Error reading config file. Invalid type supplied") # Catches any missed errors
	}
	
	# Return object
	return(mytemp)
}