Package htsjdk.beta.plugin

Interface HtsEncoder<H extends HtsHeader,R extends HtsRecord>

Type Parameters:
H - type param for the header for this encoder's format (i.e. SAMFileHeader)
R - type param for the record for this encoder's format (i.e. SAMRecord)
All Superinterfaces:
AutoCloseable, Closeable
All Known Subinterfaces:
HaploidReferenceEncoder, ReadsEncoder, VariantsEncoder
All Known Implementing Classes:
BAMEncoder, BAMEncoderV1_0, CRAMEncoder, CRAMEncoderV2_1, CRAMEncoderV3_0, SAMEncoder, SAMEncoderV1_0, VCFEncoder, VCFEncoderV3_2, VCFEncoderV3_3, VCFEncoderV4_0, VCFEncoderV4_1, VCFEncoderV4_2
public interface HtsEncoder<H extends HtsHeader,R extends HtsRecord> extends Closeable
Base interface for encoders.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
    Close any resources associated with this decoder.
    String
    getDisplayName()
    Get a user-friendly display name for this encoder.
    String
    getFileFormat()
    Get the name of the file format supported by this encoder.
    HtsVersion
    getVersion()
    Get the version of the file format supported by this encoder.
    void
    setHeader(H header)
    Set the file format header for this decoder, of type HtsEncoder.
    void
    write(R record)
    Write a single record to the underlying output.

  • Method Details

    • getFileFormat

      String getFileFormat()
      Get the name of the file format supported by this encoder. The format name defines the underlying format handled by this encoder, and also corresponds to the format of the primary bundle resource that is required when encoding (see BundleResourceType and BundleResource.getFileFormat()).
      Returns:
      the name of the underlying file format handled by this encoder

    • getVersion

      HtsVersion getVersion()
      Get the version of the file format supported by this encoder.

    • getDisplayName

      String getDisplayName()
      Get a user-friendly display name for this encoder.
      Returns:
      a user-friendly display name for this encoder for use in error and warning messages

    • setHeader

      void setHeader(H header)
      Set the file format header for this decoder, of type HtsEncoder. setHeader(HtsHeader) must be called before write(HtsRecord) can be called.
      Parameters:
      header - to use

    • write

      void write(R record)
      Write a single record to the underlying output. write(HtsRecord) may only called after setHeader(HtsHeader) has been called.
      Parameters:
      record - record to write

    • close

      void close()
      Close any resources associated with this decoder.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable