Class "headerProgram": Represention of header - program section of BAM header.

Description

headerProgram represents data contained in the header section of BAM-files.

Objects from the Class

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

Slots

l:

list

Methods

as.list

signature(x = "headerProgram"): Converts data in object into list.

getVal

signature(object = "headerProgram"): Returns value of given Segment.

setVal

signature(object = "headerProgram"): Sets value of given segment.

getHeaderText

signature(.Object = "headerProgram"): Returns textual representation of data as specified in SAM File Format.

Author(s)

Wolfgang Kaisers

References

The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011.

Examples

bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam)
isOpen(reader)
header<-getHeader(reader)
htxt<-getHeaderText(header)
headProg<-headerProgram(htxt)
getVal(headProg,"PN")
setVal(headProg,"PN","bwa")
l<-as.list(headProg)
ht<-getHeaderText(headProg)
bamClose(reader)