rbamtools (version 2.0.1)

matePosition: Read position and reference-ID of mate alignment in paired end reads from a bamAlign.

Description

Reads the position and reference-ID of mate alignment in paired end reads from a bamAlign.

Usage

matePosition(object)
mateRefID(object)

Arguments

object

An instance of class bamAlign.

Value

• matePosition, mateRefID: Integer. mateReverseStand, mateUnmapped: Logical.

References

The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011. http://www.samtools.sourceforge.net/SAM1.pdf

Examples

bam_file <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam_file)
isOpen(reader)
align<-getNextAlign(reader)
matePosition(align)
mateRefID(align)
bamClose(reader)