Rsamtools: BcfFile-class – R documentation

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BcfFile-class

Manipulate BCF files.

Description

Use BcfFile() to create a reference to a BCF (and optionally its index). The reference remains open across calls to methods, avoiding costly index re-loading.

BcfFileList() provides a convenient way of managing a list of BcfFile instances.

Usage

## Constructors

BcfFile(file, index = file,
        mode=ifelse(grepl("\\.bcf$", file), "rb", "r"))
BcfFileList(...)

## Opening / closing

## S3 method for class 'BcfFile'
open(con, ...)
## S3 method for class 'BcfFile'
close(con, ...)

## accessors; also path(), index()

## S4 method for signature 'BcfFile'
isOpen(con, rw="")
bcfMode(object)

## actions

## S4 method for signature 'BcfFile'
scanBcfHeader(file, ...)
## S4 method for signature 'BcfFile'
scanBcf(file, ..., param=ScanBcfParam())
## S4 method for signature 'BcfFile'
indexBcf(file, ...)

Arguments

`con, object`	An instance of `BcfFile`.
`file`	A character(1) vector of the BCF file path or, (for indexBcf) an instance of `BcfFile` point to a BCF file.
`index`	A character(1) vector of the BCF index.
`mode`	A character(1) vector; `mode="rb"` indicates a binary (BCF) file, `mode="r"` a text (VCF) file.
`param`	An optional `ScanBcfParam` instance to further influence scanning.
`...`	Additional arguments. For `BcfFileList`, this can either be a single character vector of paths to BCF files, or several instances of `BcfFile` objects.
`rw`	Mode of file; ignored.

Objects from the Class

Objects are created by calls of the form BcfFile().

Fields

The BcfFile class inherits fields from the RsamtoolsFile class.

Functions and methods

BcfFileList inherits methods from RsamtoolsFileList and SimpleList.

Opening / closing:

open.BcfFile: Opens the (local or remote) path and index (if bamIndex is not character(0)), files. Returns a BcfFile instance.
close.BcfFile: Closes the BcfFile con; returning (invisibly) the updated BcfFile. The instance may be re-opened with open.BcfFile.

Accessors:

path: Returns a character(1) vector of the BCF path name.
index: Returns a character(1) vector of BCF index name.
bcfMode: Returns a character(1) vector BCF mode.

Methods:

scanBcf: Visit the path in path(file), returning the result of scanBcf applied to the specified path.
show: Compactly display the object.

Author(s)

Martin Morgan

Examples

fl <- system.file("extdata", "ex1.bcf.gz", package="Rsamtools",
                  mustWork=TRUE)
bf <- BcfFile(fl)        # implicit index
bf
identical(scanBcf(bf), scanBcf(fl))

rng <- GRanges(c("seq1", "seq2"), IRanges(1, c(1575, 1584)))
param <- ScanBcfParam(which=rng)
bcf <- scanBcf(bf, param=param)  ## all ranges

## ranges one at a time 'bf'
open(bf)
sapply(seq_len(length(rng)), function(i, bcfFile, rng) {
    param <- ScanBcfParam(which=rng)
    bcf <- scanBcf(bcfFile, param=param)[[1]]
    ## do extensive work with bcf
    isOpen(bf)  ## file remains open
}, bf, rng)

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release