htsjdk.beta.codecs.reads.sam.samV1_0

Class SAMCodecV1_0

java.lang.Object

htsjdk.beta.codecs.reads.sam.SAMCodec

htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0

All Implemented Interfaces:

HtsCodec<ReadsDecoderOptions,ReadsEncoderOptions>, ReadsCodec, Upgradeable

public class SAMCodecV1_0
extends SAMCodec

SAM v1.0 codec.

Field Summary

Fields

Modifier and Type	Field and Description
static HtsVersion	VERSION_1

Constructor Summary

Constructors

Constructor and Description
SAMCodecV1_0()

Method Summary

Modifier and Type	Method and Description
SAMDecoder	getDecoder(Bundle inputBundle, ReadsDecoderOptions decoderOptions) Get an HtsDecoder to decode the provided inputs.
SAMEncoder	getEncoder(Bundle outputBundle, ReadsEncoderOptions encoderOptions) Get an HtsEncoder to encode to the provided outputs.
HtsVersion	getVersion() Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.
boolean	runVersionUpgrade(HtsVersion sourceCodecVersion, HtsVersion targetCodecVersion)

Methods inherited from class htsjdk.beta.codecs.reads.sam.SAMCodec

canDecodeSignature, canDecodeURI, getDisplayName, getFileFormat, getSignatureLength, getSignatureProbeLength, ownsURI

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.reads.ReadsCodec

getContentType

Field Detail

VERSION_1

public static final HtsVersion VERSION_1

Constructor Detail

SAMCodecV1_0

public SAMCodecV1_0()

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsCodec

Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.

Returns:

the file format version (HtsVersion) supported by this codec

getDecoder

public SAMDecoder getDecoder(Bundle inputBundle,
                             ReadsDecoderOptions decoderOptions)

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.

decoderOptions - options for the decoder to use

Returns:

an HtsDecoder that can decode the provided inputs

getEncoder

public SAMEncoder getEncoder(Bundle outputBundle,
                             ReadsEncoderOptions encoderOptions)

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

encoderOptions - encoder options to use

Returns:

an HtsEncoder suitable for writing to the provided outputs

runVersionUpgrade

public boolean runVersionUpgrade(HtsVersion sourceCodecVersion,
                                 HtsVersion targetCodecVersion)