R: 'getHeaderText' Assembling member data into Header-Text

getHeaderText-methods {rbamtools} | R Documentation

## `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

### 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.

### Value

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

### Methods

`signature(object = "bamHeader")`

  An object of class bamHeader

### 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")
    idx<-paste(bam,"bai",sep=".")
    # Open BAM file
    reader<-bamReader(bam)
    header<-getHeader(reader)
    htxt<-getHeaderText(header)
    getHeaderText(htxt)
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]