rbamtools (version 2.0.1)

bamAlign-class: Class "bamAlign"

Description

The bamAlign class represents the content of a single alignment stored in a BAM-file. An instance of this class can be created by reading an Alignment from a BAM-file. Accessor functions allow reading and writing of object contents. The alignment can be rewritten to a BAM-file via a bamWriter object.

Objects from the Class

Objects can be created by calls of the form new("bamAlign", alignment).

Examples

library(rbamtools)
bam_file <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam_file)
align<-getNextAlign(reader)
name(align)
position(align)
cigarSize(align)
cigarData(align)
bamClose(reader)