R: Class '"bamHeader"': Textual representation of header section...

bamHeaderText-class {rbamtools} | R Documentation

## Class `"bamHeader"`: Textual representation of header section of BAM files.

### Description

bamHeader manages textual representation of data contained in the header section of BAM-files. The binary representation (from which new BAM-files can be created) is encapsulated in class 'bamHeader'. Both types can be converted into each other.

### Objects from the Class

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

### Slots

`com`:

  character

`head`:

  headerLine

`dict`:

  refSeqDict

`group`:

  headerReadGroup

`prog`:

  headerProgram

### Methods

headerLine

  `signature(x = "bamHeader")`: Gets headerLine object.

headerLine<-

  `signature(x = "bamHeader")`: Sets headerLine object.

refSeqDict

  `signature(object = "bamHeader")`: Gets refSeqDict object.

refSeqDict<-

  `signature(object = "bamHeader")`: Sets refSeqDict object.

headerReadGroup

  `signature(object = "bamHeader")`: Gets headerReadGroup object.

headerReadGroup<-

  `signature(object = "bamHeader")`: Sets headerReadGroup object.

headerProgram

  `signature(.Object = "bamHeader")`: Gets headerProgram object.

headerProgram<-

  `signature(.Object = "bamHeader")`: Sets headerProgram object.

getHeaderText

  `signature(.Object = "bamHeader")`: Returns whole information encoded in a character string as described in SAM Format Specification.

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
    reader<-bamReader(bam)
    header<-getHeader(reader)
    bamClose(reader)
    htxt<-getHeaderText(header)
    headLine<-headerLine(htxt)
    headerLine(htxt)<-headLine
    readGroup<-headerReadGroup(htxt)
    headerReadGroup(htxt)<-readGroup
    headProg<-headerProgram(htxt)
    headerProgram(htxt)<-headProg
    headTxt<-getHeaderText(htxt)

[Package rbamtools version 2.16.17 Index]