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### =========================================================================
### readVcfLongForm methods
### =========================================================================
## TabixFile
msg <- paste0("'readVcfLongForm' is defunct. Use 'expand' instead. ",
"See ?'expand,CollapsedVCF-method'")
setMethod(readVcfLongForm, c(file="TabixFile", genome="character",
param="ScanVcfParam"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
.readVcfLongForm(file, genome, param)
})
setMethod(readVcfLongForm, c(file="TabixFile", genome="character",
param="GRanges"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
.readVcfLongForm(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcfLongForm, c(file="TabixFile", genome="character",
param="RangedData"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
.readVcfLongForm(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcfLongForm, c(file="TabixFile", genome="character",
param="RangesList"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
.readVcfLongForm(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcfLongForm, c(file="TabixFile", genome="character",
param="missing"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
.readVcfLongForm(file, genome, param=ScanVcfParam())
})
## character
setMethod(readVcfLongForm, c(file="character", genome="character",
param="ScanVcfParam"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
file <- .checkTabix(file)
.readVcfLongForm(file, genome, param)
})
setMethod(readVcfLongForm, c(file="character", genome="character",
param="missing"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
file <- .checkTabix(file)
.readVcfLongForm(file, genome, param=ScanVcfParam())
})
setMethod(readVcfLongForm, c(file="character", genome="missing",
param="missing"),
function(file, genome, param, ...)
{
.Defunct(msg=msg)
stop("'genome' argument is missing")
})
.checkTabix <- function(x)
{
if (1L != length(x))
stop("'x' must be character(1)")
if (grepl("\\.tbi$", x))
TabixFile(sub("\\.tbi", "", x))
else
x
}
.readVcfLongForm <- function(file, genome, param = ScanVcfParam(), ...)
{
.scanVcfToLongForm(scanVcf(file, param=param), file, genome, param)
}
.scanVcfToLongForm <- function(vcf, file, genome, param, ...)
{
hdr <- scanVcfHeader(file)
vcf <- .collapseLists(vcf, param)
## rowData
rowData <- vcf[["rowData"]]
genome(seqinfo(rowData)) <- genome
values(rowData) <- DataFrame(paramRangeID=vcf[["paramRangeID"]])
## fixed fields
ALT <- .formatALT(vcf[["ALT"]])
fx <- list(ID=names(rowData), REF=vcf[["REF"]], ALT=ALT,
QUAL=vcf[["QUAL"]], FILTER=vcf[["FILTER"]])
fixed <- DataFrame(fx[lapply(fx, is.null) == FALSE])
## info
info <- .formatInfo(vcf[["INFO"]], info(hdr))
## expand to match ALT
names(rowData) <- NULL
values(rowData) <- append(values(rowData), c(fixed, info))
rowData <- rep(rowData, elementLengths(ALT))
values(rowData)[["ALT"]] <- unlist(ALT, use.names=FALSE)
rowData
}
.formatGeno <- function(x)
{
if (length(x) == 0L)
return(list())
cls <- lapply(x, class)
nvar <- dim(x[[1]])[1]
nsmp <- dim(x[[1]])[2]
nms <- colnames(x[[1]])
## collapse matrices and arrays
for (i in which(cls == "array")) {
dim(x[[i]]) <- c(nvar*nsmp, dim(x[[i]])[3])
x[[i]] <- split(x[[i]], seq_len(nvar*nsmp))
}
for (i in which(cls == "matrix")) {
dim(x[[i]]) <- c(nvar*nsmp, 1)
}
## sample names become a data column
c(list(SAMPLES=rep(nms, each=nvar)), x)
}
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