testPairedEndBam {Rsamtools} | R 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 `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)

[Package Rsamtools version 1.32.3 Index]