Interface HtsDecoder<H extends HtsHeader,R extends HtsRecord>

Type Parameters:
H - type param for the header for this format (i.e. SAMFileHeader)
R - type param for the record for this format (i.e. SAMRecord)
All Superinterfaces:
AutoCloseable, Closeable, HtsQuery<R>, Iterable<R>
All Known Subinterfaces:
HaploidReferenceDecoder, ReadsDecoder, VariantsDecoder
All Known Implementing Classes:
BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, FASTADecoderV1_0, HtsgetBAMDecoder, HtsgetBAMDecoderV1_2, SAMDecoder, SAMDecoderV1_0, VCFDecoder, VCFDecoderV3_2, VCFDecoderV3_3, VCFDecoderV4_0, VCFDecoderV4_1, VCFDecoderV4_2, VCFDecoderV4_3

public interface HtsDecoder<H extends HtsHeader,R extends HtsRecord> extends HtsQuery<R>, Closeable
Base interface for decoders.

Implementations should not attempt to automatically resolve a companion index, and instead should only satisfy index queries when the provided input bundle explicitly specifies an index resource.

  • Method Details

    • getFileFormat

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

      HtsVersion getVersion()
      Get the version of the file format supported by this decoder.
    • getDisplayName

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

      H getHeader()
      Get the file header for this decoder.
      Returns:
      the file header for this decoder, of type H
    • close

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