@@ -419,30 +419,6 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

                              cIndexes=cIndexes, SMEDIAN=SMEDIAN,

                              theKnots=theKnots, DF=DF, probs=probs,

                              batchSize=ocProbesets())

-##   last <- 0

-##   for (idxBatch in seq(along=snpBatches)){

-##     snps <- snpBatches[[idxBatch]]

-##     rSnps <- range(snps)

-##     IndexesBatch <- list(autosomeIndex[autosomeIndex %in% snps]-last,

-##                          XIndex[XIndex %in% snps]-last,

-##                          YIndex[YIndex %in% snps]-last)

-##     IndexesBatch <- lapply(IndexesBatch, as.integer)

-##     tmpA <- A[snps,]

-##     tmpB <- B[snps,]

-##     newparamsBatch[[idxBatch]] <- gtypeCallerR(tmpA, tmpB, fIndex, mIndex,

-##                                                params[["centers"]][snps,],

-##                                                params[["scales"]][snps,],

-##                                                params[["N"]][snps,],

-##                                                IndexesBatch, cIndexes,

-##                                                sapply(IndexesBatch, length),

-##                                                sapply(cIndexes, length),

-##                                                SMEDIAN, theKnots,

-##                                                mixtureParams[], DF, probs, 0.025)

-##     last <- rSnps[2]

-##     rm(snps, rSnps, IndexesBatch, tmpA, tmpB)

-##   }

-##   rm(last)

-  

   newparams <- vector("list", 3)

   names(newparams) <- c("centers", "scales", "N")

   newparams[["centers"]] <- do.call("rbind", lapply(newparamsBatch, "[[", 1))

@@ -525,8 +501,6 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

   ## ## MOVE TO C#######

   ## running in batches

-  ## snpBatches <- splitIndicesByLength(1:nrow(A), ocProbesets())

-

   process2 <- function(idxBatch, snpBatches, autosomeIndex, XIndex,

                        YIndex, A, B, mixtureParams, fIndex, mIndex,

                        params, cIndexes, SMEDIAN, theKnots, DF, probs,

@@ -569,35 +543,6 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

            mIndex=mIndex, params=params, cIndexes=cIndexes,

            SMEDIAN=SMEDIAN, theKnots=theKnots, DF=DF, probs=probs,

            regionInfo=regionInfo, batchSize=ocProbesets())

-  

-##   last <- 0

-##   for (idxBatch in seq(along=snpBatches)){

-##     snps <- snpBatches[[idxBatch]]

-##     tmpA <- A[snps,]

-##     tmpB <- B[snps,]

-##     rSnps <- range(snps)

-##     IndexesBatch <- list(autosomeIndex[autosomeIndex %in% snps]-last,

-##                          XIndex[XIndex %in% snps]-last,

-##                          YIndex[YIndex %in% snps]-last)

-##     IndexesBatch <- lapply(IndexesBatch, as.integer)

-##     ImNull <- gtypeCallerR2(tmpA, tmpB, fIndex, mIndex,

-##                             params[["centers"]][snps,],

-##                             params[["scales"]][snps,],

-##                             params[["N"]][snps,],

-##                             IndexesBatch, cIndexes,

-##                             sapply(IndexesBatch, length),

-##                             sapply(cIndexes, length),

-##                             SMEDIAN, theKnots, mixtureParams[],

-##                             DF, probs, 0.025,

-##                             which(regionInfo[snps, 2]),

-##                             which(regionInfo[snps, 1]))

-##     A[snps,] <- tmpA

-##     B[snps,] <- tmpB

-##     last <- rSnps[2]

-##     rm(tmpA, tmpB, snps, rSnps, IndexesBatch, ImNull)

-##   }

-##   

-##   gc(verbose=FALSE)

   ##  END MOVE TO C#######

   ## ##################