rbamtools (version 2.16.17)

getHeaderText-methods: getHeaderText Assembling member data into Header-Text

Description

The header section contains various data fields which provide metadata about the stored alignment results. Returns an unparsed character string containing the header section of a BAM-file. Part of the Header-Text is the RefData information.

Usage

getHeaderText(object, delim = "\n")

Arguments

object

An object of class bamHeader or bamHeaderText

delim

Character used as tag delimiter

Value

An object of class bamHeaderText (from argument bamHeader) and a string (from argument bamHeaderText)

Methods

signature(object = "bamHeader")

An object of class bamHeader

Details

The Header section of a BAM-file consists of the header line and the Reference sequence dictionary. The header line contains information about the format version and a specification of the sorting order of alignments. The reference dictionary contains information about the name and the length of each reference sequence. The bamHeader object can be used to initialize an object of class bamWriter. The bamHeaderText can be used to inspect the content of the header.

References

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

Examples

# NOT RUN {
bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
idx<-paste(bam,"bai",sep=".")
# Open BAM file
reader<-bamReader(bam)
header<-getHeader(reader)
htxt<-getHeaderText(header)
getHeaderText(htxt)
bamClose(reader)
# }