@@ -1110,9 +1110,9 @@ construct.Illumina <- function(sampleSheet=NULL,

 	protocolData(cnSet) = protocolData

 	featureData(cnSet) = featureData

 	featureNames(cnSet) = featureNames(featureData)

-	pd = data.frame(matrix(NA, nc, 3), row.names=sampleNames(cnSet))

-	colnames(pd)=c("SKW", "SNR", "gender")

-	phenoData(cnSet) = new("AnnotatedDataFrame", data=pd)

+	##pd = data.frame(matrix(NA, nc, 3), row.names=sampleNames(cnSet))

+	##colnames(pd)=c("SKW", "SNR", "gender")

+	##phenoData(cnSet) = new("AnnotatedDataFrame", data=pd)

 	return(cnSet)

 }

@@ -1151,18 +1151,18 @@ genotype.Illumina <- function(sampleSheet=NULL,

 	if(missing(cdfName)) stop("must specify cdfName")

 	if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")

         pkgname = getCrlmmAnnotationName(cdfName)

-#        if(missing(outdir))

-#          stop("Must specify a directory to store large data objects")

-	callSet <- .GlobalEnv[["callSet"]]

-	if(is.null(callSet)){

+##        if(missing(outdir))

+##		stop("Must specify a directory to store large data objects")

+	##callSet <- .GlobalEnv[["callSet"]]

+	##if(is.null(callSet)){

 		callSet <- construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,

 					      ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,

 					      highDensity=highDensity, sep=sep, fileExt=fileExt,

 					      cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns,

 					      saveDate=saveDate) #, outdir=outdir)

 		sampleNames(callSet) <- basename(sampleNames(callSet))

-		save(callSet, file=file.path(ldPath(), "callSet.rda"))

-	} else message("Using callSet loaded from GlobalEnv")

+	##save(callSet, file=file.path(ldPath(), "callSet.rda"))

+	##} else message("Using callSet loaded from GlobalEnv")

 	if(missing(sns)) sns = basename(sampleNames(callSet))

 	if(is.lds) {

 		open(A(callSet))

@@ -1173,10 +1173,11 @@ genotype.Illumina <- function(sampleSheet=NULL,

 	snp.index = which(is.snp)

 	narrays = ncol(callSet)

 	if(is.lds) {

-		index <- .GlobalEnv[["index"]]

-		if(is.null(index)){

-			sampleBatches = splitIndicesByLength(seq(along=sampleNames(callSet)), ocSamples())

-		} else sampleBatches <- splitIndicesByLength(index, ocSamples())

+##		index <- .GlobalEnv[["index"]]

+##		if(is.null(index)){

+##			sampleBatches = splitIndicesByLength(seq(along=sampleNames(callSet)), ocSamples())

+##		} else sampleBatches <- splitIndicesByLength(seq(length=ncol(callSet)), ocSamples())

+		sampleBatches <- splitIndicesByLength(seq(length=ncol(callSet)), ocSamples())

 		mixtureParams = initializeBigMatrix("crlmmMixt-", 4, narrays, "double")

 		SNR = initializeBigVector("crlmmSNR-", narrays, "double")

 		SKW = initializeBigVector("crlmmSKW-", narrays, "double")

@@ -1190,6 +1191,7 @@ genotype.Illumina <- function(sampleSheet=NULL,

 		open(SNR)

 		pData(callSet)$SKW = SKW

 		pData(callSet)$SNR = SNR

+		save(callSet, file=file.path(ldPath(), "callSet.rda"))

 		close(SNR)

 		close(SKW)

 	} else {

@@ -1228,8 +1230,12 @@ genotype.Illumina <- function(sampleSheet=NULL,

 		open(B(callSet))

 		tmpA = initializeBigMatrix(name="tmpA", length(snp.index), narrays)

 		tmpB = initializeBigMatrix(name="tmpB", length(snp.index), narrays)

-		ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet))

-		ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet))

+		##ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet))

+		##ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet))

+		for(j in seq(length=ncol(callSet)){

+			tmpA[, j] <- as.integer(A(callSet)[snp.index, j])

+			tmpB[, j] <- as.integer(B(callSet)[snp.index, j])

+		}

 		close(A(callSet))

 		close(B(callSet))

 		close(tmpA)

@@ -1255,7 +1261,10 @@ genotype.Illumina <- function(sampleSheet=NULL,

 ##		    badSNP))

 	save(tmpA, file=file.path(ldPath(), "tmpA.rda"))

 	save(tmpB, file=file.path(ldPath(), "tmpB.rda"))

+	save(SNR, file=file.path(ldPath(), "SNR.rda"))

+	save(SKW, file=file.path(ldPath(), "SKW.rda"))

 	save(mixtureParams, file=file.path(ldPath(), "mixtureParams.rda"))

+##	return(NULL)

 	tmp <- crlmmGTfxn(FUN,

 			  A=tmpA,

 			  B=tmpB,

@@ -1282,12 +1291,15 @@ genotype.Illumina <- function(sampleSheet=NULL,

 		open(snpCallProbability(callSet))

 		ffcolapply(snpCall(callSet)[snp.index,i1:i2] <- tmp[["calls"]][,i1:i2], X=tmp[["calls"]]) #, BATCHBYTES=bb)

 		ffcolapply(snpCallProbability(callSet)[snp.index,i1:i2] <- tmp[["confs"]][,i1:i2], X=tmp[["confs"]]) #, BATCHBYTES=bb)

-#		close(tmp[["calls"]])

-#		close(tmp[["confs"]])

-		open(tmpA); open(tmpB)

+		close(tmp[["calls"]])

+		close(tmp[["confs"]])

+		close(tmpA); close(tmpB)

 		delete(tmpA); delete(tmpB);

-		delete(tmp[["calls"]]); delete(tmp[["confs"]])

-		rm(tmpA, tmpB)

+		## This line is not needed as tmp[["calls"]]

+		## is stored in tmpA and tmp[["confs"]] is stored in tmpB

+		## So deleting tmpA and tmpB in the above command removes

+		## the ff objects on disk

+		##delete(tmp[["calls"]]); delete(tmp[["confs"]])

 	} else {

 		calls(callSet)[snp.index, ] = tmp[["calls"]]

 		snpCallProbability(callSet)[snp.index, ] = tmp[["confs"]]

@@ -1302,25 +1314,25 @@ genotype.Illumina <- function(sampleSheet=NULL,

-processIDAT = function(sel, sampleSheet=NULL,

+processIDAT <- function(sel, sampleSheet=NULL,

 			arrayNames=NULL,

-			  ids=NULL,

-			  path=".",

-			  arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),

-			  highDensity=FALSE,

-			  sep="_",

-			  fileExt=list(green="Grn.idat", red="Red.idat"),

-			  saveDate=FALSE,

-			  verbose=TRUE,

+			ids=NULL,

+			path=".",

+			arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"),

+			highDensity=FALSE,

+			sep="_",

+			fileExt=list(green="Grn.idat", red="Red.idat"),

+			saveDate=FALSE,

+			verbose=TRUE,

 			mixtureSampleSize=10^5,

-			  fitMixture=TRUE,

-			  eps=0.1,

-			  seed=1,

-			  cdfName,

-			  sns,

-			  stripNorm=TRUE,

-			  useTarget=TRUE,

-              A, B, SKW, SNR, mixtureParams, is.snp) { #, outdir=".") {

+			fitMixture=TRUE,

+			eps=0.1,

+			seed=1,

+			cdfName,

+			sns,

+			stripNorm=TRUE,

+			useTarget=TRUE,

+			A, B, SKW, SNR, mixtureParams, is.snp) { #, outdir=".") {

         if(length(path)>= length(sel)) path = path[sel]

 	message("RS:... processIDAT:  calling readIdatFiles")

@@ -1353,24 +1365,41 @@ processIDAT = function(sel, sampleSheet=NULL,

 #        open(res[["mixtureParams"]])

 # remove this line: bb = ocProbesets()*length(sns)*8

 # Add these

+	##segfault came after 'Finished preprocessing', but the processIDAT loop was not yet complete

 	open(A); open(B);

-        ffcolapply(A[snp.index,sel][,i1:i2] <- res[["A"]][,i1:i2], X=res[["A"]])

-        ffcolapply(B[snp.index,sel][,i1:i2] <- res[["B"]][,i1:i2], X=res[["B"]])

+	Amatrix <- res[["A"]]

+	Bmatrix <- res[["B"]]

+	for(j in seq_along(sel)){

+		jj <- sel[j]

+		A[snp.index, jj] <- Amatrix[, j]

+		B[snp.index, jj] <- Bmatrix[, j]

+	}

+		##ffcolapply(A[snp.index,sel][,i1:i2] <- res[["A"]][,i1:i2], X=res[["A"]])

+		##ffcolapply(B[snp.index,sel][,i1:i2] <- res[["B"]][,i1:i2], X=res[["B"]])

+##	}

 #   ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, ], X=res[["A"]], BATCHBYTES=bb)

 #	ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, ], X=res[["B"]], BATCHBYTES=bb)

 	    if(length(np.index)>0) {

 #			for (j in 1:length(sel)) {

-			ffcolapply(A[np.index,sel][,i1:i2] <- res[["cnAB"]]$A[,i1:i2], X=res[["cnAB"]]$A)

-			ffcolapply(B[np.index,sel][,i1:i2] <- res[["cnAB"]]$B[,i1:i2], X=res[["cnAB"]]$B)

+		    cnAmatrix <- res[["cnAB"]]$A

+		    cnBmatrix <- res[["cnAB"]]$B

+		    for(j in seq_along(sel)){

+			    jj <- sel[j]

+			    A[np.index, jj] <- cnAmatrix[, j]

+			    B[np.index, jj] <- cnBmatrix[, j]

+		    }

+

+##			ffcolapply(A[np.index,sel][,i1:i2] <- res[["cnAB"]]$A[,i1:i2], X=res[["cnAB"]]$A)

+##			ffcolapply(B[np.index,sel][,i1:i2] <- res[["cnAB"]]$B[,i1:i2], X=res[["cnAB"]]$B)

 #            A[np.index, sel[j]] = res[["cnAB"]]$A[,j]

 #            B[np.index, sel[j]] = res[["cnAB"]]$B[,j]

 #          }

         }

 #        delete(res[["A"]]); delete(res[["B"]])

 	open(SKW); open(SNR); open(mixtureParams)

-	    SKW[sel] = res[["SKW"]][]

-	    SNR[sel] = res[["SNR"]][]

-	    mixtureParams[,sel] = res[["mixtureParams"]][]

+	SKW[sel] = res[["SKW"]][]

+	SNR[sel] = res[["SNR"]][]

+	mixtureParams[, sel] = res[["mixtureParams"]][]

         close(A)

         close(B)

         close(SNR)

@@ -1378,6 +1407,6 @@ processIDAT = function(sel, sampleSheet=NULL,

         close(mixtureParams)

 #        delete(res[["SKW"]]); delete(res[["SNR"]]); delete(res[["mixtureParams"]])

         rm(res)

-		gc()

+	gc()

         TRUE

       }