htsjdk.beta.plugin.reads

Interface ReadsCodec

All Superinterfaces:

HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>, Upgradeable

All Known Implementing Classes:

BAMCodec, BAMCodecV1_0, CRAMCodec, CRAMCodecV2_1, CRAMCodecV3_0, HtsgetBAMCodec, HtsgetBAMCodecV1_2, SAMCodec, SAMCodecV1_0

public interface ReadsCodec
extends HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>

Base class for all HtsContentType.ALIGNED_READS codecs.

Method Summary

Modifier and Type	Method and Description
default HtsContentType	getContentType() Get the HtsContentType for this codec.

Methods inherited from interface htsjdk.beta.plugin.HtsCodec

canDecodeSignature, canDecodeURI, getDecoder, getDisplayName, getEncoder, getFileFormat, getSignatureLength, getSignatureProbeLength, getVersion, ownsURI

Methods inherited from interface htsjdk.beta.plugin.Upgradeable

runVersionUpgrade

Method Detail

getContentType

default HtsContentType getContentType()

Description copied from interface: HtsCodec

Get the HtsContentType for this codec.

Specified by:

getContentType in interface HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>

Returns:

the HtsContentType for this codec. The HtsContentType determines the interfaces, including the HEADER and RECORD types, used by this codec's HtsEncoder and HtsDecoder. Each implementation of a given content type exposes the same interfaces, but over a different file format or version. For example, both the BAM and HTSGET_BAM codecs have codec type HtsContentType.ALIGNED_READS, and are derived from ReadsCodec, but the serialized file formats and access mechanisms for the two codecs are different).