testPairedEndBam: Quickly test if a BAM file has paired end reads

testPairedEndBamR Documentation

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 BamFiles 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)

Bioconductor/Rsamtools documentation built on Jan. 31, 2024, 7:12 p.m.