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

Description Usage Arguments Value Author(s) Examples

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

1

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:[email protected], Sonali Arora mailto:[email protected]

Examples

1
2
fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
testPairedEndBam(fl)

Rsamtools documentation built on Nov. 17, 2017, 1:55 p.m.