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
SAM v1.0 codec.
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptiongetDecoder
(Bundle inputBundle, ReadsDecoderOptions decoderOptions) Get anHtsDecoder
to decode the provided inputs.getEncoder
(Bundle outputBundle, ReadsEncoderOptions encoderOptions) Get anHtsEncoder
to encode to the provided outputs.Get the version of the file format returned byHtsCodec.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
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Field Details
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VERSION_1
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Constructor Details
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SAMCodecV1_0
public SAMCodecV1_0()
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Method Details
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getVersion
Description copied from interface:HtsCodec
Get the version of the file format returned byHtsCodec.getFileFormat()
that is supported by this codec.- Returns:
- the file format version (
HtsVersion
) supported by this codec
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getDecoder
Description copied from interface:HtsCodec
Get anHtsDecoder
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 anHtsCodecResolver
obtained from anHtsCodecRegistry
.The framework will never call thi* method unless either
HtsCodec.ownsURI(IOPath)
, orHtsCodec.canDecodeURI(IOPath)
andHtsCodec.canDecodeSignature(SignatureStream, String)
(IOPath)} return true forinputBundle
.- Parameters:
inputBundle
- input to be decoded. To get a decoder for use with index queries that useHtsQuery
methods, the bundle must contain an index resource.decoderOptions
- options for the decoder to use- Returns:
- an
HtsDecoder
that can decode the provided inputs
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getEncoder
Description copied from interface:HtsCodec
Get anHtsEncoder
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 anHtsCodecResolver
obtained from anHtsCodecRegistry
. The framework will never call this method unless eitherHtsCodec.ownsURI(IOPath)
, orHtsCodec.canDecodeURI(IOPath)
returned true foroutputBundle
.- Parameters:
outputBundle
- target output for the encoderencoderOptions
- encoder options to use- Returns:
- an
HtsEncoder
suitable for writing to the provided outputs
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runVersionUpgrade
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