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### =========================================================================
### readVcf methods
### =========================================================================
## TabixFile
setMethod(readVcf, c(file="TabixFile", genome="ANY",
param="ScanVcfParam"),
function(file, genome, param, ...)
{
.readVcf(file, genome, param)
})
setMethod(readVcf, c(file="TabixFile", genome="ANY",
param="GRanges"),
function(file, genome, param, ...)
{
.readVcf(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcf, c(file="TabixFile", genome="ANY",
param="RangedData"),
function(file, genome, param, ...)
{
.readVcf(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcf, c(file="TabixFile", genome="ANY",
param="GRangesList"),
function(file, genome, param, ...)
{
.readVcf(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcf, c(file="TabixFile", genome="ANY",
param="RangesList"),
function(file, genome, param, ...)
{
.readVcf(file, genome, param=ScanVcfParam(which=param))
})
setMethod(readVcf, c(file="TabixFile", genome="ANY",
param="missing"),
function(file, genome, param, ...)
{
.readVcf(file, genome, param=ScanVcfParam())
})
## character
setMethod(readVcf, c(file="character", genome="ANY",
param="ScanVcfParam"),
function(file, genome, param, ...)
{
file <- .checkFile(file)
.readVcf(file, genome, param)
})
setMethod(readVcf, c(file="character", genome="ANY",
param="missing"),
function(file, genome, param, ...)
{
file <- .checkFile(file)
.readVcf(file, genome, param=ScanVcfParam())
})
setMethod(readVcf, c(file="character", genome="missing",
param="missing"),
function(file, genome, param, ...)
{
stop("'genome' argument is missing")
})
.checkFile <- function(x)
{
if (1L != length(x))
stop("'x' must be character(1)")
## Tabix index supplied as 'file'
if (grepl("\\.tbi$", x))
return(TabixFile(sub("\\.tbi", "", x)))
## Attempt to create TabixFile
tryCatch(x <- TabixFile(x), error=function(e) return(x))
x
}
.readVcf <- function(file, genome, param, ...)
{
if (!is(genome, "character") & !is(genome, "Seqinfo"))
stop("'genome' must be a 'character(1)' or 'Seqinfo' object")
if (is(genome, "Seqinfo")) {
if (is(param, "ScanVcfParam"))
chr <- names(vcfWhich(param))
else
chr <- seqlevels(param)
if (any(!chr %in% seqnames(genome)))
stop("'seqnames' in 'vcfWhich(param)' must be present in 'genome'")
}
.scanVcfToVCF(scanVcf(file, param=param), file, genome, param)
}
.scanVcfToVCF <- function(vcf, file, genome, param, ...)
{
hdr <- scanVcfHeader(file)
if (length(vcf[[1]]$GENO) > 0L)
colnms <- colnames(vcf[[1]]$GENO[[1]])
else
colnms <- NULL
vcf <- .collapseLists(vcf, param)
## rowData
rowData <- vcf$rowData
seqinfo(rowData) <- merge(seqinfo(rowData), seqinfo(hdr))
if (length(rowData)) {
if (is(genome, "character")) {
genome(rowData) <- genome
} else {
oldsi <- seqinfo(rowData)
newsi <- genome
if (length(newsi) > length(oldsi)) {
new2old <- match(seqlevels(newsi), seqlevels(oldsi))
seqinfo(rowData, new2old=new2old) <- merge(newsi, oldsi)
} else {
seqinfo(rowData) <- genome
}
}
}
values(rowData) <- DataFrame(vcf["paramRangeID"])
## fixed fields
fx <- vcf[c("REF", "ALT", "QUAL", "FILTER")]
fx$ALT <- .formatALT(fx$ALT)
fixed <- DataFrame(fx[!sapply(fx, is.null)])
## info
info <- .formatInfo(vcf$INFO, info(hdr), length(rowData))
## colData
colData <- DataFrame(Samples=seq_along(colnms), row.names=colnms)
## geno
geno <- SimpleList(lapply(vcf$GENO, `dimnames<-`, NULL))
vcf <- NULL
VCF(rowData=rowData, colData=colData, exptData=SimpleList(header=hdr),
fixed=fixed, info=info, geno=geno)
}
## lightweight read functions retrieve a single variable
readInfo <- function(file, x, param=ScanVcfParam(), ..., row.names=TRUE)
{
lst <- .readLite(file, x, param, "info")
rowData <- lst$rowData
res <- .formatInfo(lst$INFO, info(scanVcfHeader(file)),
length(rowData))[[1]]
if (row.names)
names(res) <- names(rowData)
res
}
readGeno <- function(file, x, param=ScanVcfParam(), ..., row.names=TRUE)
{
lst <- .readLite(file, x, param, "geno")
rowData <- lst$rowData
res <- lst$GENO[[1]]
if (row.names)
dimnames(res)[[1]] <- names(rowData)
res
}
readGT <- function(file, nucleotides=FALSE, param=ScanVcfParam(), ...,
row.names=TRUE)
{
lst <- .readLite(file, "GT", param, "GT")
if (nucleotides)
res <- .geno2geno(lst, row.names=row.names)
else
res <- lst$GENO$GT
rowData <- lst$rowData
if (row.names)
dimnames(res)[[1]] <- names(rowData)
res
}
.geno2geno <- function(lst, row.names)
{
## ignore records with GT ".|."
ALT <- lst$ALT
REF <- as.character(lst$REF, use.names=FALSE)
GT <- res <- lst$GENO$GT
if (any(missing <- grepl(".", GT, fixed=TRUE)))
GT[missing] <- ".|."
phasing <- rep("|", length(GT))
phasing[grepl("/", GT, fixed=TRUE)] <- "/"
## replace
GTstr <- strsplit(as.vector(GT), "[|,/]")
if (any(elementLengths(GTstr) !=2))
stop("only diploid variants are supported")
GTmat <- matrix(unlist(GTstr), ncol=2, byrow=TRUE)
GTA <- suppressWarnings(as.numeric(GTmat[,1]))
GTB <- suppressWarnings(as.numeric(GTmat[,2]))
REFcs <- cumsum(elementLengths(REF))
ALTcs <- cumsum(elementLengths(ALT))
cs <- REFcs + c(0, head(ALTcs, -1))
offset <- rep(cs, ncol(res))
alleles <- unlist(rbind(REF,ALT), use.names=FALSE)
alleleA <- alleles[offset + GTA]
alleleB <- alleles[offset + GTB]
if (any(missing)) {
res[!missing] <- paste0(alleleA[!missing],
phasing[!missing],
alleleB[!missing])
} else {
res[] <- paste0(alleleA, phasing, alleleB)
}
res
}
.readLite <- function(file, var, param, type, ...)
{
msg <- NULL
if (!is.character(var))
msg <- c(msg, paste0("'", var, "'", " must be a character string"))
if (length(var) > 1L)
msg <- c(msg, paste0("'", var, "'", " must be of length 1"))
if (!is.null(msg))
stop(msg)
if (is(param, "ScanVcfParam")) {
which <- vcfWhich(param)
samples <- vcfSamples(param)
} else {
which <- param
samples <- character()
}
if (type == "info")
param=ScanVcfParam(NA, var, NA, which=which)
else if (type == "geno")
param=ScanVcfParam(NA, NA, var, samples, which=which)
else if (type == "GT")
param=ScanVcfParam("ALT", NA, var, samples, which=which)
scn <- scanVcf(file, param=param)
.collapseLists(scn, param)
}
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