rbamtools (version 2.4.0)

getNextAlign-methods: getNextAlign: Retrieving next align from bamReader or bamRange

Description

Returns an object of class bamAlign from bamReader or bamRange.

Value

• An object of class bamAlign or NULL.

Examples

library(rbamtools)
bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
idx<-system.file("extdata","accepted_hits.bam.bai",package="rbamtools")
reader<-bamReader(bam)
isOpen(reader)
align<-getNextAlign(reader)
if(is.null(align))
	print("End of File!
")
load.index(reader,idx)
index.initialized(reader)
coords<-as.integer(c(0,0,249250621))
range<-bamRange(reader,coords)
align<-getNextAlign(range)
position(align)
bamClose(reader)