Nothing
.scanBamTemplate <-
function(seqlevels=factor(), tag=character(0))
{
.Call(.scan_bam_template, seqlevels, tag)
}
.scanBam_template <-
function(file, param)
{
tmpl <- .scanBamTemplate(factor(levels=seqlevels(file)), bamTag(param))
## set those elements of the template that are not 'tag' (treat
## specially because nested list) nor specified by 'what'
## parameter to NULL
tmpl[!names(tmpl) %in% c(bamWhat(param), "tag")] <- list(NULL)
if (0L == length(tmpl[["tag"]]))
tmpl["tag"] <- list(NULL)
tmpl
}
## return rname:start-end values for outer list elements
.scanBam_extract_which_labels <- function(param) {
which <- bamWhich(param)
if( 0L != length(space(which)))
paste0(space(which), ":", .uunlist(start(which)), "-",
.uunlist(end(which)))
else
NULL
}
.scanBam_postprocess <-
function(x, param)
{
which <- bamWhich(param)
if (0L != length(space(which)))
names(x) <-
paste0(space(which), ":", .uunlist(start(which)), "-",
.uunlist(end(which)))
lapply(x, Filter, f=Negate(is.null))
}
setMethod(scanBam, "character",
function(file, index=file, ...,
param=ScanBamParam(what=scanBamWhat()))
{
if (missing(index) && 0L == length(bamWhich(param)))
index <- character(0)
bam <- open(BamFile(file, index), "rb")
on.exit(close(bam))
scanBam(bam, ..., param=param)
})
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