Rsamtools: testPairedEndBam – R documentation

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testPairedEndBam

Quickly test if a BAM file has paired end reads

Description

Iterate through a BAM file until a paired-end read is encountered or the end of file is reached; report the occurrence of paired-end reads to the user.

Usage

testPairedEndBam(file, index=file, ...)

Arguments

`file`	character(1) BAM file name, or a `BamFile` instance. Open `BamFile`s are closed; their yield size is respected when iterating through the file.
`index`	(optional) character(1) name of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
`...`	Additional arguments, currently unused.

Value

A logical vector of length 1 containing TRUE is returned if BAM file contained paired end reads, FALSE otherwise.

Author(s)

Martin Morgan mailto:mtmorgan@fhcrc.org, Sonali Arora mailto:sarora@fhcrc.org

Examples

fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
testPairedEndBam(fl)

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