Nothing
.header <- function(file)
{
if (is(file, "RangedVcfStack")) {
header <- scanVcfHeader(files(file)[[1]])
} else {
header <- scanVcfHeader(file)
}
header
}
.availableNames_msg <- function(file)
{
avail <- vcfFields(file)
msg <- paste(
'The available values for "name" argument are: \n',
"fixed(", length(avail$fixed), "): ",
paste(avail$fixed, collapse = " "), "\n",
"info(", length(avail$info), "): ",
paste(avail$info, collapse = " "), "\n",
"geno(", length(avail$geno), "): ",
paste(avail$geno, collapse = " "), "\n",
sep = "")
msg
}
.pfixFun <- function(x)
{
get(x, envir = getNamespace("VariantAnnotation"))
}
## For generating an R null object of type ... in VCF.
.get_VCFArraySeed_type <- function(seed, pfix, name)
{
hdr <- .header(vcffile(seed))
if (pfix %in% c("info", "geno")) {
tp <- .pfixFun(pfix)(hdr)[name, "Type"]
} else if (name %in% c("REF", "ALT", "FILTER")) {
tp <- "Character"
} else if (name == "QUAL") {
tp <- "Float"
} else {
return(NULL)
}
map <- c(Integer = "integer", Float = "numeric", Flag = "character",
String = "character", Character = "character")
tp <- map[tp]
tp
}
.get_VCFArraySeed_basic_param <- function(seed, pfix, name)
{
if (pfix == "geno") {
param <- ScanVcfParam(fixed = NA, info = NA, geno = name)
} else if (pfix == "info") {
param <- ScanVcfParam(fixed = NA, info = name, geno = NA)
} else if (pfix == "fixed" && name == "REF") {
param <- ScanVcfParam(fixed = NA, info = NA, geno = NA)
} else if (pfix == "fixed") {
param <- ScanVcfParam(fixed = name, info = NA, geno = NA)
} else {
return(NULL)
}
param
}
.readVcf_for_class <- function(vcf, param, pfix, name)
{
if(is(vcf, "VcfFile")) {
res <- readVcf(vcf, genome = "hg19", param = param)
} else if (is(vcf, "RangedVcfStack")) {
res <- readVcfStack(vcf, param = param)
}
res <- .pfixFun(pfix)(res)[[name]]
if(is(res, "XStringSetList")) {
res <- array(res@unlistData)
}else if (is(res, "list_OR_List")) {
res <- array(res)
}
res
}
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