rbamtools (version 2.0.1)

bamWriter-class: Class "bamWriter"

Description

Encapsulates functionality to write bamAligns to BAM-file.

Objects from the Class

Objects can be created by calls of the form writer<-bamWriter(reader,filename).

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

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)
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)