rbamtools (version 2.0.1)

bamSave: bamSave(bamAlign)

Description

Saves an object of class bamAlignment or bamRange to a BAM-file via an Instance of class bamWriter.

Usage

bamSave(object, ...)

Arguments

object

An Instance of class bamWriter

...

An Instance of class bamAlign or bamRange

Value

• None

Examples

library(rbamtools)
bam_file <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
idx_file <- system.file("extdata", "accepted_hits.bam.bai", package="rbamtools")
reader<-bamReader(bam_file)
isOpen(reader)
align<-getNextAlign(reader)
loadIndex(reader,idx_file)
coords<-as.integer(c(0,0,1874))
index.initialized(reader)
range<-bamRange(reader,coords)
writer<-bamWriter(reader,"test.bam")
bamSave(writer,align)
bamSave(writer,range)
bamClose(reader)
bamClose(writer)