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

In Bioconductor/Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

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:[e-mail], Sonali Arora mailto:[e-mail]

Examples

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

Bioconductor/Rsamtools documentation built on May 2, 2024, 11:20 p.m.