Package htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2

Class HtsgetBAMCodecV1_2

java.lang.Object

htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec

htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMCodecV1_2

All Implemented Interfaces:

HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>, ReadsCodec, Upgradeable

public class HtsgetBAMCodecV1_2
extends HtsgetBAMCodec

Version 1.2 of BundleResourceType.READS_HTSGET_BAM codec.

Field Summary

Fields inherited from class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec

HTSGET_VERSION

Constructor Summary

Constructors

Constructor	Description
HtsgetBAMCodecV1_2()

Method Summary

Modifier and Type	Method	Description
HtsgetBAMDecoder	getDecoder(Bundle inputBundle, ReadsDecoderOptions decodeOptions)	Get an HtsDecoder to decode the provided inputs.
HtsEncoder<?,? extends HtsRecord>	getEncoder(Bundle outputBundle, ReadsEncoderOptions encodeOptions)	Get an HtsEncoder to encode to the provided outputs.

Methods inherited from class htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec

canDecodeSignature, canDecodeURI, getFileFormat, getSignatureLength, getVersion, handlesURI, ownsURI, runVersionUpgrade

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.beta.plugin.HtsCodec

getDisplayName, getSignatureProbeLength

Methods inherited from interface htsjdk.beta.plugin.reads.ReadsCodec

getContentType

Constructor Details

HtsgetBAMCodecV1_2

public HtsgetBAMCodecV1_2()

Method Details

getDecoder

public HtsgetBAMDecoder getDecoder(Bundle inputBundle,
 ReadsDecoderOptions decodeOptions)

Description copied from interface: HtsCodec

Get an HtsDecoder to decode the provided inputs. The input bundle must contain resources of the type required by this codec. To find a codec appropriate for decoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

The framework will never call thi* method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) and HtsCodec.canDecodeSignature(SignatureStream, String) (IOPath)} return true for inputBundle.

Parameters:

inputBundle - input to be decoded. To get a decoder for use with index queries that use HtsQuery methods, the bundle must contain an index resource.

decodeOptions - options for the decoder to use

Returns:

an HtsDecoder that can decode the provided inputs

getEncoder

public HtsEncoder<?,? extends HtsRecord> getEncoder(Bundle outputBundle,
 ReadsEncoderOptions encodeOptions)

Description copied from interface: HtsCodec

Get an HtsEncoder to encode to the provided outputs. The output bundle must contain resources of the type required by this codec. To find a codec appropriate for encoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

The framework will never call this method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) returned true for outputBundle.

Parameters:

outputBundle - target output for the encoder

encodeOptions - encoder options to use

Returns:

an HtsEncoder suitable for writing to the provided outputs