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rbamtools (version 2.0.1)

getHeaderText: Reads Header section Text of BAM-file.

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 = "")
object{An object of class bamReader}
  delim{Character used as tag delimiter}

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.

Character string.
[object Object]
The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011.
http://www.samtools.sourceforge.net/SAM1.pdf
getRefData
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)
if(isOpen(reader))
	header<-getHeaderText(reader)
# ...
bamClose(reader)
bamReader
bamHeader

Arguments