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setMethod(asSam, "character",
function(file, destination=sub("\\.bam", "", file), ..., overwrite=FALSE)
{
file <- .normalizePath(file)
destination <- .normalizePath(destination)
d0 <- paste(destination, "sam", sep=".")
if (!overwrite && file.exists(d0)) {
msg <- sprintf("'%s' exists, '%s' is FALSE\n %s: %s",
"destination", "overwrite", "destination",
d0)
stop(msg)
}
tryCatch({
result <- .Call(.as_bam, file, d0, FALSE)
if (!file.exists(d0))
stop("failed to create 'SAM' file")
}, error=function(err) {
msg <- sprintf("'asSam' %s\n SAM file: '%s'\n",
conditionMessage(err), file)
stop(msg)
})
d0
})
setMethod(asBam, "character",
function(file, destination=sub("\\.sam(\\.gz)?", "", file), ...,
overwrite=FALSE, indexDestination=TRUE)
{
file <- .normalizePath(file)
destination <- .normalizePath(destination)
d0 <- paste(destination, "bam", sep=".")
ofl <- tempfile()
on.exit(unlink(ofl))
if (!overwrite && file.exists(d0)) {
msg <- sprintf("'%s' exists, '%s' is FALSE\n %s: %s",
"destination", "overwrite", "destination",
d0)
stop(msg)
}
tryCatch({
result <- .Call(.as_bam, file, ofl, TRUE)
if (!file.exists(ofl))
stop("failed to create 'BAM' file")
if (indexDestination) {
destination <- sortBam(ofl, destination)
indexBam(destination)
} else {
destination <- d0
.file.rename(ofl, destination)
}
}, error=function(err) {
msg <- sprintf("'asBam' %s\n SAM file: '%s'\n",
conditionMessage(err), file)
stop(msg)
})
destination
})
|
