Class

au.csiro.variantspark.input

ExtendedVCFCodec

Related Doc: package input

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class ExtendedVCFCodec extends VCFCodec

Linear Supertypes
VCFCodec, AbstractVCFCodec, NameAwareCodec, AsciiFeatureCodec[VariantContext], AbstractFeatureCodec[VariantContext, LineIterator], FeatureCodec[VariantContext, LineIterator], AnyRef, Any
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  2. By Inheritance
Inherited
  1. ExtendedVCFCodec
  2. VCFCodec
  3. AbstractVCFCodec
  4. NameAwareCodec
  5. AsciiFeatureCodec
  6. AbstractFeatureCodec
  7. FeatureCodec
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new ExtendedVCFCodec()

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Type Members

  1. class LazyVCFGenotypesParser extends LazyParser

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    Attributes
    private[htsjdk.variant.vcf]
    Definition Classes
    AbstractVCFCodec

Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def canDecode(arg0: String): Boolean

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    Definition Classes
    VCFCodec → FeatureCodec

  6. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  7. def close(arg0: LineIterator): Unit

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    Definition Classes
    AsciiFeatureCodec → FeatureCodec

  8. def createGenotypeMap(arg0: String, arg1: List[Allele], arg2: String, arg3: Int): LazyData

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    Definition Classes
    AbstractVCFCodec

  9. def decode(arg0: String): VariantContext

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    Definition Classes
    AbstractVCFCodec → AsciiFeatureCodec

  10. def decode(arg0: LineIterator): VariantContext

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    Definition Classes
    AsciiFeatureCodec → FeatureCodec

  11. def decodeLoc(arg0: String): htsjdk.tribble.Feature

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    Definition Classes
    AbstractVCFCodec

  12. def decodeLoc(arg0: LineIterator): htsjdk.tribble.Feature

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    Definition Classes
    AbstractFeatureCodec → FeatureCodec
    Annotations
    @throws( classOf[java.io.IOException] )

  13. final def disableOnTheFlyModifications(): Unit

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    Definition Classes
    AbstractVCFCodec

  14. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  16. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  17. def generateException(arg0: String): Unit

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    Attributes
    protected[htsjdk.variant.vcf]
    Definition Classes
    AbstractVCFCodec

  18. def getCachedString(arg0: String): String

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    Attributes
    protected[htsjdk.variant.vcf]
    Definition Classes
    AbstractVCFCodec

  19. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  20. def getFeatureType(): Class[VariantContext]

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    Definition Classes
    AbstractFeatureCodec → FeatureCodec

  21. def getName(): String

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    Definition Classes
    AbstractVCFCodec → NameAwareCodec

  22. def getVersion(): VCFHeaderVersion

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  23. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  24. def isDone(arg0: LineIterator): Boolean

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    Definition Classes
    AsciiFeatureCodec → FeatureCodec

  25. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  26. def makeIndexableSourceFromStream(arg0: InputStream): LocationAware

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    Definition Classes
    AsciiFeatureCodec → FeatureCodec

  27. def makeSourceFromStream(arg0: InputStream): LineIterator

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    Definition Classes
    AsciiFeatureCodec → FeatureCodec

  28. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  29. final def notify(): Unit

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    Definition Classes
    AnyRef

  30. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  31. def parseFilters(arg0: String): List[String]

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    Attributes
    protected[htsjdk.variant.vcf]
    Definition Classes
    VCFCodec → AbstractVCFCodec

  32. def parseHeaderFromLines(arg0: List[String], arg1: VCFHeaderVersion): VCFHeader

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    Attributes
    protected[htsjdk.variant.vcf]
    Definition Classes
    AbstractVCFCodec

  33. def readActualHeader(arg0: LineIterator): AnyRef

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    Definition Classes
    VCFCodec → AsciiFeatureCodec

  34. def readHeader(arg0: LineIterator): FeatureCodecHeader

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    Definition Classes
    AsciiFeatureCodec → FeatureCodec
    Annotations
    @throws( classOf[java.io.IOException] )

  35. def setName(arg0: String): Unit

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    Definition Classes
    AbstractVCFCodec → NameAwareCodec

  36. def setRemappedSampleName(arg0: String): Unit

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    Definition Classes
    AbstractVCFCodec

  37. def setVCFHeader(arg0: VCFHeader, arg1: VCFHeaderVersion): VCFHeader

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    Definition Classes
    AbstractVCFCodec

  38. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  39. def toString(): String

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    Definition Classes
    AnyRef → Any

  40. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  41. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  42. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from VCFCodec

Inherited from AbstractVCFCodec

Inherited from NameAwareCodec

Inherited from AsciiFeatureCodec[VariantContext]

Inherited from AbstractFeatureCodec[VariantContext, LineIterator]

Inherited from FeatureCodec[VariantContext, LineIterator]

Inherited from AnyRef

Inherited from Any

Ungrouped