rbamtools (version 2.4.0)

bamHeader-class: Class "bamHeader"

Description

bamHeader represents Data contained in the header Section of BAM-files.

Objects from the Class

Objects can be created by calls of the form header<-new("bamHeader").

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

bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
# Open bam file
reader<-bamReader(bam)
# Extract binary header structure
header<-getHeader(reader)
# Extract textual representation
htxt<-getHeaderText(header)
# Extract header line segment
hl<-headerLine(htxt)
# Re-create binary header structure
header2<-bamHeader(htxt)
# Use created structure for new BAM-file
writer<-bamWriter(header2,"test.bam")
bamClose(reader)
bamClose(writer)