insertSize: insertSize: Reads insert size from bamAlign

Description

Reads the core.isize field from an alignment. Insert size should represent the distance between mate pair reads (but this is not explicitly declared in the format documentation).

Usage

insertSize(object)

Arguments

object

An instance of class bamAlign.

Value

Integer.

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

Run this code

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

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