A base class for managing file references in Rsamtools

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Description

RsamtoolsFile is a base class for managing file references in Rsamtools; it is not intended for direct use by users – see, e.g., BamFile.

Usage

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## accessors
index(object)
## S4 method for signature 'RsamtoolsFile'
path(object, ...)
## S4 method for signature 'RsamtoolsFile'
isOpen(con, rw="")
## S4 method for signature 'RsamtoolsFile'
yieldSize(object, ...)
yieldSize(object, ...) <- value
## S4 method for signature 'RsamtoolsFile'
show(object)

Arguments

con, object

An instance of a class derived from RsamtoolsFile.

rw

Mode of file; ignored.

...

Additional arguments, unused.

value

Replacement value.

Objects from the Class

Users do not directly create instances of this class; see, e.g., BamFile-class.

Fields

The RsamtoolsFile class is implemented as an S4 reference class. It has the following fields:

.extptr

An externalptr initialized to an internal structure with opened bam file and bam index pointers.

path

A character(1) vector of the file name.

index

A character(1) vector of the index file name.

yieldSize

An integer(1) vector of the number of records to yield.

Functions and methods

Accessors:

path

Returns a character(1) vector of path names.

index

Returns a character(1) vector of index path names.

yieldSize, yieldSize<-

Return or set an integer(1) vector indicating yield size.

Methods:

isOpen

Report whether the file is currently open.

show

Compactly display the object.

Author(s)

Martin Morgan

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