R: Class '"bamHeader"': Representation of data contained in the...

bamHeader-class {rbamtools} | R Documentation

## Class `"bamHeader"`: Representation of data contained in the header section of BAM files.

### Description

bamHeader represents data contained in the header Section of BAM-files.

### Objects from the Class

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

### Slots

`header`:

  Object of class `"externalptr"`. Points to samtools bam_header_t struct.

### Methods

getHeaderText

  `signature(x = "bamHeader")`: Returns textual representation of data stored in this class as desrcribed in SAM Format Specification.

### 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")
    # Open bam file
    reader<-bamReader(bam)
    # Extract binary header structure
    header<-getHeader(reader)
    header
    # Extract textual representation
    htxt<-getHeaderText(header)
    # Extract header line segment
    hl<-headerLine(htxt)
    # Get header program
    hp<-headerProgram(htxt)
    hp
    # Re-create binary header structure
    header2<-bamHeader(htxt)
    # Use created structure for new BAM-file

    writer<-bamWriter(header2,"test.bam")
    bamClose(reader)
    bamClose(writer)

[Package rbamtools version 2.16.17 Index]