Package 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
Base class for all
HtsContentType.ALIGNED_READS
codecs.-
Method Summary
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 Details
-
getContentType
Description copied from interface:HtsCodec
Get theHtsContentType
for this codec.- Specified by:
getContentType
in interfaceHtsCodec<ReadsDecoderOptions,
ReadsEncoderOptions> - Returns:
- the
HtsContentType
for this codec. TheHtsContentType
determines the interfaces, including the HEADER and RECORD types, used by this codec'sHtsEncoder
andHtsDecoder
. 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 typeHtsContentType.ALIGNED_READS
, and are derived fromReadsCodec
, but the serialized file formats and access mechanisms for the two codecs are different).
-