Class

org.apache.spark.rdd

VariantContextWithHeader

Related Doc: package rdd

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class VariantContextWithHeader extends VariantContext

Linear Supertypes
VariantContext, Serializable, Feature, Locatable, AnyRef, Any
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Inherited
  1. VariantContextWithHeader
  2. VariantContext
  3. Serializable
  4. Feature
  5. Locatable
  6. AnyRef
  7. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new VariantContextWithHeader(context: VariantContext, header: VCFHeader)

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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 calcVCFGenotypeKeys(arg0: VCFHeader): List[String]

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    Definition Classes
    VariantContext

  6. def clone(): AnyRef

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

  7. def contains(arg0: Locatable): Boolean

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    Definition Classes
    Locatable

  8. val context: VariantContext

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  9. def contigsMatch(arg0: Locatable): Boolean

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    Definition Classes
    Locatable

  10. def emptyID(): Boolean

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    Definition Classes
    VariantContext

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

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    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  13. def extraStrictValidation(arg0: Allele, arg1: Allele, arg2: Set[String]): Unit

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    Definition Classes
    VariantContext

  14. def filtersWereApplied(): Boolean

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    Definition Classes
    VariantContext

  15. def finalize(): Unit

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

  16. def fullyDecode(arg0: VCFHeader, arg1: Boolean): VariantContext

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    Definition Classes
    VariantContext

  17. def getAllele(arg0: Array[Byte]): Allele

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    Definition Classes
    VariantContext

  18. def getAllele(arg0: String): Allele

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    Definition Classes
    VariantContext

  19. def getAlleleIndex(arg0: Allele): Int

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    Definition Classes
    VariantContext

  20. def getAlleleIndices(arg0: Collection[Allele]): List[Integer]

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    Definition Classes
    VariantContext

  21. def getAlleles(): List[Allele]

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    Definition Classes
    VariantContext

  22. def getAltAlleleWithHighestAlleleCount(): Allele

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    Definition Classes
    VariantContext

  23. def getAlternateAllele(arg0: Int): Allele

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    Definition Classes
    VariantContext

  24. def getAlternateAlleles(): List[Allele]

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    Definition Classes
    VariantContext

  25. def getAttribute(arg0: String, arg1: Any): AnyRef

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    Definition Classes
    VariantContext

  26. def getAttribute(arg0: String): AnyRef

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    Definition Classes
    VariantContext

  27. def getAttributeAsBoolean(arg0: String, arg1: Boolean): Boolean

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    Definition Classes
    VariantContext

  28. def getAttributeAsDouble(arg0: String, arg1: Double): Double

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    Definition Classes
    VariantContext

  29. def getAttributeAsDoubleList(arg0: String, arg1: Double): List[Double]

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    Definition Classes
    VariantContext

  30. def getAttributeAsInt(arg0: String, arg1: Int): Int

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    Definition Classes
    VariantContext

  31. def getAttributeAsIntList(arg0: String, arg1: Int): List[Integer]

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    Definition Classes
    VariantContext

  32. def getAttributeAsList(arg0: String): List[AnyRef]

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    Definition Classes
    VariantContext

  33. def getAttributeAsString(arg0: String, arg1: String): String

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    Definition Classes
    VariantContext

  34. def getAttributeAsStringList(arg0: String, arg1: String): List[String]

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    Definition Classes
    VariantContext

  35. def getAttributes(): Map[String, AnyRef]

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    Definition Classes
    VariantContext

  36. def getCalledChrCount(arg0: Allele, arg1: Set[String]): Int

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    Definition Classes
    VariantContext

  37. def getCalledChrCount(arg0: Allele): Int

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    Definition Classes
    VariantContext

  38. def getCalledChrCount(arg0: Set[String]): Int

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    Definition Classes
    VariantContext

  39. def getCalledChrCount(): Int

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    Definition Classes
    VariantContext

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

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    Definition Classes
    AnyRef → Any

  41. def getCommonInfo(): CommonInfo

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    Definition Classes
    VariantContext

  42. def getContig(): String

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    Definition Classes
    VariantContext → Locatable

  43. def getEnd(): Int

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    Definition Classes
    VariantContext → Locatable

  44. def getFilters(): Set[String]

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    Definition Classes
    VariantContext

  45. def getFiltersMaybeNull(): Set[String]

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    Definition Classes
    VariantContext

  46. def getGLIndicesOfAlternateAllele(arg0: Allele): Array[Int]

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    Definition Classes
    VariantContext

  47. def getGenotype(arg0: Int): Genotype

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    Definition Classes
    VariantContext

  48. def getGenotype(arg0: String): Genotype

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    Definition Classes
    VariantContext

  49. def getGenotypes(arg0: Set[String]): GenotypesContext

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    Definition Classes
    VariantContext

  50. def getGenotypes(arg0: Collection[String]): GenotypesContext

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    Attributes
    protected[htsjdk.variant.variantcontext]
    Definition Classes
    VariantContext

  51. def getGenotypes(arg0: String): GenotypesContext

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    Definition Classes
    VariantContext

  52. def getGenotypes(): GenotypesContext

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    Definition Classes
    VariantContext

  53. def getGenotypesOrderedBy(arg0: Iterable[String]): Iterable[Genotype]

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    Definition Classes
    VariantContext

  54. def getGenotypesOrderedByName(): Iterable[Genotype]

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    Definition Classes
    VariantContext

  55. def getHeader: VCFHeader

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  56. def getHetCount(): Int

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    Definition Classes
    VariantContext

  57. def getHomRefCount(): Int

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    Definition Classes
    VariantContext

  58. def getHomVarCount(): Int

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    Definition Classes
    VariantContext

  59. def getID(): String

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    Definition Classes
    VariantContext

  60. def getIndelLengths(): List[Integer]

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    Definition Classes
    VariantContext

  61. def getLengthOnReference(): Int

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    Definition Classes
    Locatable

  62. def getLog10PError(): Double

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    Definition Classes
    VariantContext

  63. def getMaxPloidy(arg0: Int): Int

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    Definition Classes
    VariantContext

  64. def getMixedCount(): Int

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    Definition Classes
    VariantContext

  65. def getNAlleles(): Int

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    Definition Classes
    VariantContext

  66. def getNSamples(): Int

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    Definition Classes
    VariantContext

  67. def getNoCallCount(): Int

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    Definition Classes
    VariantContext

  68. def getPhredScaledQual(): Double

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    Definition Classes
    VariantContext

  69. def getReference(): Allele

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    Definition Classes
    VariantContext

  70. def getSampleNames(): Set[String]

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    Definition Classes
    VariantContext

  71. def getSampleNamesOrderedByName(): List[String]

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    Definition Classes
    VariantContext

  72. def getSource(): String

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    Definition Classes
    VariantContext

  73. def getStart(): Int

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    Definition Classes
    VariantContext → Locatable

  74. def getStructuralVariantType(): StructuralVariantType

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    Definition Classes
    VariantContext

  75. def getType(): Type

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    Definition Classes
    VariantContext

  76. def getVariantContext: VariantContext

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  77. def hasAllele(arg0: Allele, arg1: Boolean): Boolean

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    Definition Classes
    VariantContext

  78. def hasAllele(arg0: Allele): Boolean

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    Definition Classes
    VariantContext

  79. def hasAlternateAllele(arg0: Allele, arg1: Boolean): Boolean

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    Definition Classes
    VariantContext

  80. def hasAlternateAllele(arg0: Allele): Boolean

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    Definition Classes
    VariantContext

  81. def hasAttribute(arg0: String): Boolean

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    Definition Classes
    VariantContext

  82. def hasGenotype(arg0: String): Boolean

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    Definition Classes
    VariantContext

  83. def hasGenotypes(arg0: Collection[String]): Boolean

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    Definition Classes
    VariantContext

  84. def hasGenotypes(): Boolean

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    Definition Classes
    VariantContext

  85. def hasID(): Boolean

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    Definition Classes
    VariantContext

  86. def hasLog10PError(): Boolean

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    Definition Classes
    VariantContext

  87. def hasSameAllelesAs(arg0: VariantContext): Boolean

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    Definition Classes
    VariantContext

  88. def hasSameAlternateAllelesAs(arg0: VariantContext): Boolean

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    Definition Classes
    VariantContext

  89. def hasSymbolicAlleles(): Boolean

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    Definition Classes
    VariantContext

  90. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  91. val header: VCFHeader

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  92. def isBiallelic(): Boolean

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    Definition Classes
    VariantContext

  93. def isComplexIndel(): Boolean

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    Definition Classes
    VariantContext

  94. def isFiltered(): Boolean

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    Definition Classes
    VariantContext

  95. def isFullyDecoded(): Boolean

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    Definition Classes
    VariantContext

  96. def isIndel(): Boolean

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    Definition Classes
    VariantContext

  97. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  98. def isMNP(): Boolean

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    Definition Classes
    VariantContext

  99. def isMixed(): Boolean

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    Definition Classes
    VariantContext

  100. def isMonomorphicInSamples(): Boolean

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    Definition Classes
    VariantContext

  101. def isNotFiltered(): Boolean

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    Definition Classes
    VariantContext

  102. def isPointEvent(): Boolean

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    Definition Classes
    VariantContext

  103. def isPolymorphicInSamples(): Boolean

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    Definition Classes
    VariantContext

  104. def isReferenceBlock(): Boolean

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    Definition Classes
    VariantContext

  105. def isSNP(): Boolean

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    Definition Classes
    VariantContext

  106. def isSimpleDeletion(): Boolean

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    Definition Classes
    VariantContext

  107. def isSimpleIndel(): Boolean

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    Definition Classes
    VariantContext

  108. def isSimpleInsertion(): Boolean

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    Definition Classes
    VariantContext

  109. def isStructuralIndel(): Boolean

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    Definition Classes
    VariantContext

  110. def isSymbolic(): Boolean

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    Definition Classes
    VariantContext

  111. def isSymbolicOrSV(): Boolean

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    Definition Classes
    VariantContext

  112. def isVariant(): Boolean

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    Definition Classes
    VariantContext

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

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    Definition Classes
    AnyRef

  114. final def notify(): Unit

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    Definition Classes
    AnyRef

  115. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  116. def overlaps(arg0: Locatable): Boolean

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    Definition Classes
    Locatable

  117. def subContextFromSample(arg0: String): VariantContext

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    Definition Classes
    VariantContext

  118. def subContextFromSamples(arg0: Set[String]): VariantContext

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    Definition Classes
    VariantContext

  119. def subContextFromSamples(arg0: Set[String], arg1: Boolean): VariantContext

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    Definition Classes
    VariantContext

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

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    Definition Classes
    AnyRef

  121. def toString(): String

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    Definition Classes
    VariantContext → AnyRef → Any

  122. def toStringDecodeGenotypes(): String

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    Definition Classes
    VariantContext

  123. def toStringWithoutGenotypes(): String

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    Definition Classes
    VariantContext

  124. def validateAlternateAlleles(): Unit

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    Definition Classes
    VariantContext

  125. def validateChromosomeCounts(): Unit

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    Definition Classes
    VariantContext

  126. def validateRSIDs(arg0: Set[String]): Unit

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    Definition Classes
    VariantContext

  127. def validateReferenceBases(arg0: Allele, arg1: Allele): Unit

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    Definition Classes
    VariantContext

  128. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  131. def withinDistanceOf(arg0: Locatable, arg1: Int): Boolean

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    Definition Classes
    Locatable

Deprecated Value Members

  1. def getChr(): String

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    Definition Classes
    Feature
    Annotations
    @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

  2. def getGLIndecesOfAlternateAllele(arg0: Allele): Array[Int]

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    Definition Classes
    VariantContext
    Annotations
    @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from VariantContext

Inherited from Serializable

Inherited from Feature

Inherited from Locatable

Inherited from AnyRef

Inherited from Any

Ungrouped