BcfFile-class: Manipulate BCF files.

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

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 documentation built on Nov. 8, 2020, 8:11 p.m.