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PileupFiles <-
function(files, ..., param=ApplyPileupsParam())
{
bfl <- BamFileList(files, ...)
new("PileupFiles", bfl, param=param)
}
plpFiles <- function(object) as(object, "BamFileList")
plpParam <- function(object) object@param
setMethod(applyPileups, c("PileupFiles", "ApplyPileupsParam"),
function(files, FUN, ..., param)
{
FUN <- match.fun(FUN)
ok <- isOpen(files)
if (!all(ok))
if (any(ok))
stop("all(isOpen(<PileupFiles>))' is not 'TRUE'")
else {
open(files)
on.exit(close(files))
}
lvls <- lapply(files, seqlevels)
for (i in seq_along(files)[-1])
if (!identical(lvls[[i]], lvls[[1]])) {
msg <- sprintf("applyPileups 'seqlevels' must be identical();
failed when comparing %s with %s",
sQuote(basename(path(files)[1])),
sQuote(basename(path(files)[i])))
stop(paste(strwrap(msg, exdent=4), collapse="\n"))
}
tryCatch({
param <- as(param, "list")
extptr <- lapply(files, .extptr)
regions <-
if (0L != length(param[["which"]])) .asRegions(param[["which"]])
else NULL
param[["what"]] <- c("seq", "qual") %in% param[["what"]]
.Call(.apply_pileups, extptr, names(files), regions, param, FUN)
}, error=function(err) {
stop("applyPileups: ", conditionMessage(err), call.=FALSE)
})
})
setMethod(applyPileups, c("PileupFiles", "missing"),
function(files, FUN, ..., param)
{
applyPileups(files, FUN, ..., param=plpParam(files))
})
setMethod(show, "PileupFiles", function(object) {
cat("class:", class(object), "\n")
nms <- names(object)
txt <- paste(S4Vectors:::selectSome(nms, 3L), collapse=", ")
cat(sprintf("names: %s (%d total)\n", txt, length(nms)))
fls <- sapply(object, function(x) basename(path(x)))
txt <- paste(S4Vectors:::selectSome(fls, 3L), collapse=", ")
cat(sprintf("plpFiles: %s (%d total)\n", txt, length(fls)))
cat("plpParam: class", class(plpParam(object)), "\n")
})
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