rbamtools (version 2.0.1)

bamWriter: bamWriter Object

Description

bamWriter represents a writing connection to a BAM-file

Usage

bamWriter(reader,filename)

Arguments

reader

bamWriter imports header data (Reference table and metadata) from reader.

filename

Filename of BAM-file to be opened for writing.

Examples

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)
index.initialized(reader)
coords<-as.integer(c(0,0,1874))
range<-bamRange(reader,coords)

writer<-bamWriter(reader,"test.bam")
bamSave(writer,align)
bamSave(writer,range)

bamClose(reader)
bamClose(writer)