R: Class '"headerProgram"': Represention of header - program...

headerProgram-class {rbamtools} | R Documentation

## 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)

[Package rbamtools version 2.16.17 Index]