@@ -303,7 +303,7 @@ appendGDSgenotypeMat <- function(gds, matG) {

 generateGDS1KGgenotypeFromSNPPileup <- function(pathGeno,

     listSamples, listPos, offset, minCov=10, minProb=0.999,

     seqError=0.001, pedStudy, batch, studyDF, PATHGDSSAMPLE=NULL,

-    genoSource = c("snp-pileup", "generic"), verbose) {

+    genoSource=c("snp-pileup", "generic"), verbose) {

     # File with the description of the SNP keep

     listMat <- dir(pathGeno, pattern = ".+.txt.gz")

@@ -322,7 +322,7 @@ generateGDS1KGgenotypeFromSNPPileup <- function(pathGeno,

             if(genoSource == "snp-pileup") {

                 matSample <- readSNVPileupFile(file.path(pathGeno,

                                         listMat[pos]), offset)

-            } else if(genoTypeSource == "generic") {

+            } else if(genoSource == "generic") {

                 matSample <- readSNVFileGeneric(file.path(pathGeno,

                                         listMat[pos]), offset)

             }

@@ -53,6 +53,15 @@

 #' the directory where the Profile GDS files will be created.

 #' Default: \code{NULL}.

 #'

+#' @param genoSource a \code{stirng} with two possible values:

+#' snp-pileup and generic. It specify if the genotype files

+#' are generate by snp-pileup(Facets) or generic format csv

+#' with the column at least the columns:

+#' Chromosome,Position,Ref,Alt,Count,File1R,File1A

+#' where Count is the deep at the position,

+#' FileR is the deep of the reference allele, and

+#' File1A is the deep of the specific alternative allele

+#'

 #' @param verbose a \code{logical} indicating if message information should be

 #' printed. Default: \code{FALSE}.

 #'

@@ -87,7 +96,9 @@

 #' result <- createStudy2GDS1KG(pathGeno=dataDir,

 #'             pedStudy=samplePED, fileNameGDS=fileGDS,

 #'             studyDF=studyDF, listProfiles=c("ex1"),

-#'             pathProfileGDS=dataDir, verbose=FALSE)

+#'             pathProfileGDS=dataDir,

+#'             genoSource="snp-pileup",

+#'             verbose=FALSE)

 #'

 #' ## The function returns OL when successful

 #' result

@@ -107,7 +118,9 @@

 createStudy2GDS1KG <- function(pathGeno=file.path("data", "sampleGeno"),

                                 fileNamePED=NULL, pedStudy=NULL, fileNameGDS,

                                 batch=1, studyDF, listProfiles=NULL,

-                                pathProfileGDS=NULL, verbose=FALSE) {

+                                pathProfileGDS=NULL,

+                                genoSource=c("snp-pileup", "generic"),

+                                verbose=FALSE) {

     ## When fileNamePED is defined and pedStudy is null

     if (!(is.null(fileNamePED)) && is.null(pedStudy)) {

@@ -130,7 +143,9 @@ createStudy2GDS1KG <- function(pathGeno=file.path("data", "sampleGeno"),

     validateCreateStudy2GDS1KG(pathGeno=pathGeno, pedStudy=pedStudy,

         fileNameGDS=fileNameGDS, batch=batch, studyDF=studyDF,

         listProfiles=listProfiles, pathProfileGDS=pathProfileGDS,

-        verbose=verbose)

+        genoSource=genoSource, verbose=verbose)

+

+    genoSource <- match.arg(genoSource)

     ## Read the 1KG GDS file

     gds <- snpgdsOpen(filename=fileNameGDS)

@@ -151,7 +166,8 @@ createStudy2GDS1KG <- function(pathGeno=file.path("data", "sampleGeno"),

     generateGDS1KGgenotypeFromSNPPileup(pathGeno=pathGeno,

         listSamples=listProfiles, listPos=listPos, offset=-1, minCov=10,

         minProb=0.999, seqError=0.001, pedStudy=pedStudy, batch=batch,

-        studyDF=studyDF, PATHGDSSAMPLE=pathProfileGDS, verbose=verbose)

+        studyDF=studyDF, PATHGDSSAMPLE=pathProfileGDS,

+        genoSource=genoSource, verbose=verbose)

     if(verbose) {

         message("Genotype DONE ", Sys.time())

@@ -2177,6 +2193,15 @@ computeAncestryFromSyntheticFile <- function(gds, gdsSample,

 #' super-population assigned to the sample. }

 #' }

 #'

+#' @param genoSource a \code{stirng} with two possible values:

+#' snp-pileup and generic. It specify if the genotype files

+#' are generate by snp-pileup(Facets) or generic format csv

+#' with the column at least the columns:

+#' Chromosome,Position,Ref,Alt,Count,File1R,File1A

+#' where Count is the deep at the position,

+#' FileR is the deep of the reference allele, and

+#' File1A is the deep of the specific alternative allele

+#'

 #' @return The integer \code{0L} when successful. See details section for

 #' more information about the generated output files.

 #'

@@ -2285,7 +2310,8 @@ computeAncestryFromSyntheticFile <- function(gds, gdsSample,

 #'                     fileReferenceGDS=fileReferenceGDS,

 #'                     fileReferenceAnnotGDS=fileAnnotGDS,

 #'                     chrInfo=chrInfo,

-#'                     dataRefSyn=dataRef)

+#'                     dataRefSyn=dataRef,

+#'                     genoSource="snp-pileup")

 #'

 #' unlink(pathProfileGDS, recursive=TRUE, force=TRUE)

 #' unlink(pathOut, recursive=TRUE, force=TRUE)

@@ -2297,19 +2323,23 @@ computeAncestryFromSyntheticFile <- function(gds, gdsSample,

 #' @export

 runExomeAncestry <- function(pedStudy, studyDF, pathProfileGDS,

                     pathGeno, pathOut, fileReferenceGDS, fileReferenceAnnotGDS,

-                        chrInfo, dataRefSyn) {

+                    chrInfo, dataRefSyn,

+                    genoSource=c("snp-pileup", "generic")) {

     ## Validate parameters

     validateRunExomeAncestry(pedStudy, studyDF, pathProfileGDS,

         pathGeno=pathGeno, pathOut=pathOut, fileReferenceGDS=fileReferenceGDS,

         fileReferenceAnnotGDS=fileReferenceAnnotGDS, chrInfo=chrInfo,

-        dataRefSyn=dataRefSyn)

+        dataRefSyn=dataRefSyn, genoSource=genoSource)

+

+    genoSource <- match.arg(genoSource)

     listProfiles <- pedStudy[, "Name.ID"]

     createStudy2GDS1KG(pathGeno=pathGeno, pedStudy=pedStudy,

                 fileNameGDS=fileReferenceGDS, listProfiles=listProfiles,

-                studyDF=studyDF, pathProfileGDS=pathProfileGDS)

+                studyDF=studyDF, pathProfileGDS=pathProfileGDS,

+                genoSource=genoSource, verbose=FALSE)

     ## Open the 1KG GDS file (demo version)

     gds1KG <- snpgdsOpen(fileReferenceGDS)

@@ -501,14 +501,16 @@ validateEstimateAllelicFraction <- function(gds, gdsSample, currentProfile,

 #' RAIDS:::validateCreateStudy2GDS1KG(pathGeno=dataDir, pedStudy=ped,

 #'             fileNameGDS=gds1KG, batch=1, studyDF=studyInfo,

 #'             listProfiles=c("Sample_01", "Sample_02"),

-#'             pathProfileGDS=dataDir, verbose=TRUE)

+#'             pathProfileGDS=dataDir,

+#'             genoSource="snp-pileup", verbose=TRUE)

 #'

 #' @author Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

 #' @importFrom S4Vectors isSingleNumber

 #' @encoding UTF-8

 #' @keywords internal

 validateCreateStudy2GDS1KG <- function(pathGeno, pedStudy, fileNameGDS, batch,

-                            studyDF, listProfiles, pathProfileGDS, verbose) {

+                            studyDF, listProfiles, pathProfileGDS,

+                            genoSource, verbose) {

     ## The pathGeno must be a existing directory

     if (!dir.exists(pathGeno)) {

@@ -544,6 +546,11 @@ validateCreateStudy2GDS1KG <- function(pathGeno, pedStudy, fileNameGDS, batch,

                 " the path where the Profile GDS files will be generated.")

     }

+    ## The genoSource must be a character string

+    if(!(is.character(genoSource))) {

+        stop("The \'genoSource\' parameter must be a character string.")

+    }

+

     ## The verbose parameter must be a logical

     validateLogical(logical=verbose, "verbose")

@@ -1052,14 +1059,14 @@ validateAdd1KG2SampleGDS <- function(gds, gdsProfileFile, currentProfile,

 #' RAIDS:::validateRunExomeAncestry(pedStudy=ped, studyDF=study,

 #'     pathProfileGDS=dataDir, pathGeno=dataDir, pathOut=pathOut,

 #'     fileReferenceGDS=gds1KG, fileReferenceAnnotGDS=gdsAnnot1KG,

-#'     chrInfo=chrInfo, dataRefSyn=dataRefSyn)

+#'     chrInfo=chrInfo, dataRefSyn=dataRefSyn, genoSource="snp-pileup")

 #'

 #' @author Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

 #' @encoding UTF-8

 #' @keywords internal

 validateRunExomeAncestry <- function(pedStudy, studyDF, pathProfileGDS,

     pathGeno, pathOut, fileReferenceGDS, fileReferenceAnnotGDS,

-    chrInfo, dataRefSyn) {

+    chrInfo, dataRefSyn, genoSource) {

     ## The PED study must have the mandatory columns

     validatePEDStudyParameter(pedStudy=pedStudy)

@@ -1093,12 +1100,18 @@ validateRunExomeAncestry <- function(pedStudy, studyDF, pathProfileGDS,

                 "The file must exist.")

     }

+

     ## The chrInfo must be a vector of integer

     validatePositiveIntegerVector(chrInfo, "chrInfo")

     ## The dataRefSyn must have the madatory columns

     validateDataRefSynParameter(dataRefSyn=dataRefSyn)

+    ## The genoSource must be a character string

+    if(!(is.character(genoSource))) {

+        stop("The \'genoSource\' parameter must be a character string.")

+    }

+

     return(0L)

 }

@@ -16,6 +16,7 @@ createStudy2GDS1KG(

   studyDF,

   listProfiles = NULL,

   pathProfileGDS = NULL,

+  genoSource = c("snp-pileup", "generic"),

   verbose = FALSE

 )

 }

@@ -66,6 +67,15 @@ Default: \code{NULL}.}

 the directory where the Profile GDS files will be created.

 Default: \code{NULL}.}

+\item{genoSource}{a \code{stirng} with two possible values:

+snp-pileup and generic. It specify if the genotype files

+are generate by snp-pileup(Facets) or generic format csv

+with the column at least the columns:

+Chromosome,Position,Ref,Alt,Count,File1R,File1A

+where Count is the deep at the position,

+FileR is the deep of the reference allele, and

+File1A is the deep of the specific alternative allele}

+

 \item{verbose}{a \code{logical} indicating if message information should be

 printed. Default: \code{FALSE}.}

 }

@@ -107,7 +117,9 @@ rownames(samplePED) <- samplePED$Name.ID

 result <- createStudy2GDS1KG(pathGeno=dataDir,

             pedStudy=samplePED, fileNameGDS=fileGDS,

             studyDF=studyDF, listProfiles=c("ex1"),

-            pathProfileGDS=dataDir, verbose=FALSE)

+            pathProfileGDS=dataDir,

+            genoSource="snp-pileup",

+            verbose=FALSE)

 ## The function returns OL when successful

 result

@@ -14,7 +14,8 @@ runExomeAncestry(

   fileReferenceGDS,

   fileReferenceAnnotGDS,

   chrInfo,

-  dataRefSyn

+  dataRefSyn,

+  genoSource = c("snp-pileup", "generic")

 )

 }

 \arguments{

@@ -63,6 +64,15 @@ subcontinental population assigned to the sample. }

 \item{superPop} { a \code{character} string representing the

 super-population assigned to the sample. }

 }}

+

+\item{genoSource}{a \code{stirng} with two possible values:

+snp-pileup and generic. It specify if the genotype files

+are generate by snp-pileup(Facets) or generic format csv

+with the column at least the columns:

+Chromosome,Position,Ref,Alt,Count,File1R,File1A

+where Count is the deep at the position,

+FileR is the deep of the reference allele, and

+File1A is the deep of the specific alternative allele}

 }

 \value{

 The integer \code{0L} when successful. See details section for

@@ -168,7 +178,8 @@ runExomeAncestry(pedStudy=ped, studyDF=studyDF,

                     fileReferenceGDS=fileReferenceGDS,

                     fileReferenceAnnotGDS=fileAnnotGDS,

                     chrInfo=chrInfo,

-                    dataRefSyn=dataRef)

+                    dataRefSyn=dataRef,

+                    genoSource="snp-pileup")

 unlink(pathProfileGDS, recursive=TRUE, force=TRUE)

 unlink(pathOut, recursive=TRUE, force=TRUE)

@@ -13,6 +13,7 @@ validateCreateStudy2GDS1KG(

   studyDF,

   listProfiles,

   pathProfileGDS,

+  genoSource,

   verbose

 )

 }

@@ -86,7 +87,8 @@ ped <- data.frame(Name.ID=c("Sample_01", "Sample_02"),

 RAIDS:::validateCreateStudy2GDS1KG(pathGeno=dataDir, pedStudy=ped,

             fileNameGDS=gds1KG, batch=1, studyDF=studyInfo,

             listProfiles=c("Sample_01", "Sample_02"),

-            pathProfileGDS=dataDir, verbose=TRUE)

+            pathProfileGDS=dataDir,

+            genoSource="snp-pileup", verbose=TRUE)

 }

 \author{

@@ -14,7 +14,8 @@ validateRunExomeAncestry(

   fileReferenceGDS,

   fileReferenceAnnotGDS,

   chrInfo,

-  dataRefSyn

+  dataRefSyn,

+  genoSource

 )

 }

 \arguments{

@@ -112,7 +113,7 @@ dataRefSyn <- data.frame(sample.id=c("HG00150", "HG00138", "HG00330",

 RAIDS:::validateRunExomeAncestry(pedStudy=ped, studyDF=study,

     pathProfileGDS=dataDir, pathGeno=dataDir, pathOut=pathOut,

     fileReferenceGDS=gds1KG, fileReferenceAnnotGDS=gdsAnnot1KG,

-    chrInfo=chrInfo, dataRefSyn=dataRefSyn)

+    chrInfo=chrInfo, dataRefSyn=dataRefSyn, genoSource="snp-pileup")

 }

 \author{

@@ -1413,7 +1413,8 @@ test_that(paste0("createStudy2GDS1KG() must return error when fileNamePED is",

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

             fileNamePED=33, pedStudy=NULL, fileNameGDS=NULL,

             batch=1, studyDF=NULL, listProfiles=NULL,

-            pathProfileGDS=NULL, verbose=TRUE), error_message)

+            pathProfileGDS=NULL,

+            genoSource="snp-pileup", verbose=TRUE), error_message)

 })

@@ -1425,7 +1426,8 @@ test_that("createStudy2GDS1KG() must return error when fileNamePED is NULL and p

     expect_error(createStudy2GDS1KG(pathGeno=file.path("data", "sampleGeno"),

                     fileNamePED=NULL, pedStudy=NULL, fileNameGDS=NULL,

                     batch=1, studyDF=NULL, listProfiles=NULL,

-                    pathProfileGDS=NULL, verbose=TRUE), error_message)

+                    pathProfileGDS=NULL,

+                    genoSource="snp-pileup", verbose=TRUE), error_message)

 })

@@ -1444,7 +1446,8 @@ test_that("createStudy2GDS1KG() must return error when pedDF is missing mandator

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

                     fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=NULL,

                     batch=1, studyDF=NULL, listProfiles=NULL,

-                    pathProfileGDS=NULL, verbose=TRUE), error_message)

+                    pathProfileGDS=NULL,

+                    genoSource="snp-pileup", verbose=TRUE), error_message)

 })

@@ -1464,7 +1467,8 @@ test_that("createStudy2GDS1KG() must return error when fileNameGDS is numerical

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

                         fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=33,

                         batch=1, studyDF=NULL, listProfiles=NULL,

-                        pathProfileGDS=NULL, verbose=TRUE), error_message)

+                        pathProfileGDS=NULL,

+                        genoSource="snp-pileup", verbose=TRUE), error_message)

 })

@@ -1484,7 +1488,8 @@ test_that("createStudy2GDS1KG() must return error when batch is character string

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

             fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=fileGDS,

             batch="1", studyDF=NULL, listProfiles=NULL,

-            pathProfileGDS=NULL, verbose=TRUE), error_message)

+            pathProfileGDS=NULL,

+            genoSource="snp-pileup", verbose=TRUE), error_message)

 })

@@ -1504,7 +1509,8 @@ test_that("createStudy2GDS1KG() must return error when batch is vector of numeri

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

                 fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=fileGDS,

                 batch=c(1,2), studyDF=NULL, listProfiles=NULL,

-                pathProfileGDS=NULL, verbose=TRUE), error_message)

+                pathProfileGDS=NULL,

+                genoSource="snp-pileup", verbose=TRUE), error_message)

 })

@@ -1528,7 +1534,8 @@ test_that("createStudy2GDS1KG() must return error when listSamples is vector of

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

             fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=fileGDS,

             batch=1, studyDF=studyDF, listProfiles=c(1,2),

-            pathProfileGDS=NULL, verbose=TRUE), error_message, fixed=TRUE)

+            pathProfileGDS=NULL,

+            genoSource="snp-pileup", verbose=TRUE), error_message, fixed=TRUE)

 })

@@ -1552,7 +1559,8 @@ test_that("createStudy2GDS1KG() must return error when listProfiles is numeric",

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

         fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=fileGDS,

         batch=1, studyDF=studyDF, listProfiles=1,

-        pathProfileGDS=NULL, verbose=TRUE), error_message, fixed=TRUE)

+        pathProfileGDS=NULL,

+        genoSource="snp-pileup", verbose=TRUE), error_message, fixed=TRUE)

 })

@@ -1577,7 +1585,8 @@ test_that("createStudy2GDS1KG() must return error when studyDF is missing column

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

         fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=fileGDS,

         batch=1, studyDF=studyDF, listProfiles=1,

-        pathProfileGDS=NULL, verbose=TRUE), error_message, fixed=TRUE)

+        pathProfileGDS=NULL,

+        genoSource="snp-pileup", verbose=TRUE), error_message, fixed=TRUE)

 })

@@ -1600,7 +1609,8 @@ test_that("createStudy2GDS1KG() must return error when verbose is numeric", {

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

             fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=fileGDS,

             batch=1, studyDF=studyDF, listProfiles=NULL,

-            pathProfileGDS=dataDir, verbose=22), error_message, fixed=TRUE)

+            pathProfileGDS=dataDir,

+            genoSource="snp-pileup", verbose=22), error_message, fixed=TRUE)

 })

@@ -1625,7 +1635,8 @@ test_that("createStudy2GDS1KG() must return error when pathProfileGDS is numeric

     expect_error(createStudy2GDS1KG(pathGeno=dataDir,

         fileNamePED=NULL, pedStudy=pedDF, fileNameGDS=gdsFile,

         batch=1, studyDF=studyDF, listProfiles=NULL,

-        pathProfileGDS=33, verbose=FALSE), error_message, fixed=TRUE)

+        pathProfileGDS=33,

+        genoSource="snp-pileup", verbose=FALSE), error_message, fixed=TRUE)

 })

@@ -1649,7 +1660,8 @@ test_that("createStudy2GDS1KG() must return error when both fileNamePED and pedS

     expect_error(createStudy2GDS1KG(pathGeno=file.path("data", "sampleGeno"),

                 fileNamePED=fileGDS, pedStudy=pedDF, fileNameGDS=fileGDS,

                 batch=1, studyDF=studyDF, listProfiles=NULL,

-                pathProfileGDS=dataDir, verbose=22), error_message, fixed=TRUE)

+                pathProfileGDS=dataDir,

+                genoSource="snp-pileup", verbose=22), error_message, fixed=TRUE)

 })

@@ -1675,7 +1687,8 @@ test_that("createStudy2GDS1KG() must return expected results when all parameters

     result <- createStudy2GDS1KG(pathGeno=dataDir,

                 pedStudy=pedDF, fileNameGDS=fileGDS,

                 batch=1, studyDF=studyDF, listProfiles=c("ex1"),

-                pathProfileGDS=dataDir, verbose=FALSE)

+                pathProfileGDS=dataDir,

+                genoSource="snp-pileup", verbose=FALSE)

     expect_true(file.exists(file.path(dataDir, "ex1.gds")))

     expect_equal(result, 0L)

@@ -2332,7 +2345,8 @@ test_that(paste0("runExomeAncestry() must return error when pathOut is numeric")

         pathProfileGDS=pathOut,

         pathGeno=pathOut, pathOut=33, fileReferenceGDS=fileGDS,

         fileReferenceAnnotGDS=gdsFileAnnot, chrInfo=chrInfo,

-        dataRefSyn=dataRefSyn), error_message)

+        dataRefSyn=dataRefSyn,

+        genoSource="snp-pileup"), error_message)

 })

@@ -2364,7 +2378,8 @@ test_that(paste0("runExomeAncestry() must return error when fileReferenceGDS is

     expect_error(runExomeAncestry(pedStudy=ped, studyDF=studyDF,

         pathProfileGDS=pathOut, pathGeno=pathOut, pathOut=pathOut,

         fileReferenceGDS=33, fileReferenceAnnotGDS=gdsFileAnnot,

-        chrInfo=chrInfo, dataRefSyn), error_message)

+        chrInfo=chrInfo, dataRefSyn,

+        genoSource="snp-pileup"), error_message)

 })

@@ -2397,7 +2412,8 @@ test_that(paste0("runExomeAncestry() must return error when fileReferenceAnnotGD

     expect_error(runExomeAncestry(pedStudy=ped, studyDF=studyDF,

             pathProfileGDS=pathOut, pathGeno=pathOut, pathOut=pathOut,

             fileReferenceGDS=fileGDS, fileReferenceAnnotGDS=32,

-            chrInfo=chrInfo, dataRefSyn=dataRefSyn), error_message)

+            chrInfo=chrInfo, dataRefSyn=dataRefSyn,

+            genoSource="snp-pileup"), error_message)

 })

@@ -2428,7 +2444,8 @@ test_that(paste0("runExomeAncestry() must return error when chrInfo is vector of

     expect_error(runExomeAncestry(pedStudy=ped, studyDF=studyDF,

         pathProfileGDS=pathOut, pathGeno=pathOut, pathOut=pathOut,

         fileReferenceGDS=fileGDS, fileReferenceAnnotGDS=gdsFileAnnot,

-        chrInfo=c("ALLO", "TEST"), dataRefSyn=dataRefSyn), error_message)

+        chrInfo=c("ALLO", "TEST"), dataRefSyn=dataRefSyn,

+        genoSource="snp-pileup"), error_message)

 })

@@ -2461,7 +2478,8 @@ test_that(paste0("runExomeAncestry() must return error when dataRefSyn missing c

     expect_error(runExomeAncestry(pedStudy=ped, studyDF=studyDF,

         pathProfileGDS=pathOut, pathGeno=pathOut, pathOut=pathOut,

         fileReferenceGDS=fileGDS, fileReferenceAnnotGDS=gdsFileAnnot,

-        chrInfo=c(100L, 200L), dataRefSyn=dataRefSyn), error_message)

+        chrInfo=c(100L, 200L), dataRefSyn=dataRefSyn,

+        genoSource="snp-pileup"), error_message)

 })

@@ -2491,5 +2509,6 @@ test_that(paste0("runExomeAncestry() must return error when pathGeno does not ex

     expect_error(runExomeAncestry(pedStudy=ped, studyDF=studyDF,

         pathProfileGDS=pathOut, pathGeno="DONOTEXISTDIR", pathOut=pathOut,

         fileReferenceGDS=fileGDS, fileReferenceAnnotGDS=gdsFileAnnot,

-        chrInfo=c(100L, 200L), dataRefSyn=dataRefSyn), error_message)

+        chrInfo=c(100L, 200L), dataRefSyn=dataRefSyn,

+        genoSource="snp-pileup"), error_message)

 })

@@ -80,7 +80,7 @@ test_that("validateCreateStudy2GDS1KG() must return expected results when all in

     result1 <- RAIDS:::validateCreateStudy2GDS1KG(pathGeno=dataDir,

             pedStudy=ped, fileNameGDS=fileGDS, batch=12, studyDF=studyInfo,

             listProfiles=c("TCGA-H01", "TCGA-H02"), pathProfileGDS=dataDir,

-            verbose=TRUE)

+            genoSource="snp-pileup", verbose=TRUE)

     expect_identical(result1, 0L)

 })

@@ -224,7 +224,7 @@ test_that("validateRunExomeAncestry() must return expected results when all inpu

     result <- RAIDS:::validateRunExomeAncestry(pedStudy=ped, studyDF=studyInfo,

         pathProfileGDS=dataDir, pathGeno=dataDir, pathOut=dataDir,

         fileReferenceGDS=gdsRefFile, fileReferenceAnnotGDS=gdsRefAnnotFile,

-        chrInfo=chrInfo, dataRefSyn=dataRefSyn)

+        chrInfo=chrInfo, dataRefSyn=dataRefSyn, genoSource="snp-pileup")

     expect_identical(result, 0L)

 })

@@ -421,7 +421,8 @@ createStudy2GDS1KG(pathGeno = pathGeno,

                         fileNameGDS = file.GDS,

                         listProfiles = listSamples,

                         studyDF = studyDF,

-                        pathProfileGDS = pathProfileGDS)

+                        pathProfileGDS = pathProfileGDS,

+                        genoSource="snp-pileup")

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

 ## The Sample GDS file has been created in the 

@@ -1096,7 +1097,8 @@ runExomeAncestry(pedStudy=ped, studyDF=studyDF,

                  fileReferenceGDS=fileGDS,

                  fileReferenceAnnotGDS=fileAnnotGDS,

                  chrInfo=chrInfo,

-                 dataRefSyn=dataRef)

+                 dataRefSyn=dataRef,

+                 genoSource="snp-pileup")

 list.files(pathOut)

 list.files(file.path(pathOut, ped$Name.ID[1]))