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org.bdgenomics.adam.converters

DefaultHeaderLines

object DefaultHeaderLines

Default set of VCF header lines for INFO and GT format fields supported in ADAM.

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  1. final def !=(arg0: Any): Boolean
    Definition Classes
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  2. final def ##(): Int
    Definition Classes
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  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. lazy val allHeaderLines: Seq[VCFHeaderLine]

    Default set of VCF header lines for INFO and GT format fields supported in ADAM.

  5. lazy val alleleCount: VCFInfoHeaderLine
  6. lazy val alleleFrequency: VCFInfoHeaderLine
  7. lazy val allelicDepth: VCFFormatHeaderLine
  8. lazy val ancestralAllele: VCFInfoHeaderLine
  9. final def asInstanceOf[T0]: T0
    Definition Classes
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  10. lazy val cigar: VCFInfoHeaderLine
  11. def clone(): AnyRef
    Attributes
    protected[lang]
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    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  12. lazy val dbSnp: VCFInfoHeaderLine
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
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  14. def equals(arg0: Any): Boolean
    Definition Classes
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  15. lazy val fisherStrand: VCFFormatHeaderLine
  16. lazy val formatHeaderLines: Seq[VCFFormatHeaderLine]

    Default set of VCF header lines for GT format fields supported in ADAM.

  17. lazy val formatReadDepth: VCFFormatHeaderLine
  18. lazy val forwardReadDepth: VCFInfoHeaderLine
  19. lazy val genotype: VCFFormatHeaderLine
  20. lazy val genotypeFilter: VCFFormatHeaderLine
  21. lazy val genotypeQuality: VCFFormatHeaderLine
  22. final def getClass(): Class[_]
    Definition Classes
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    Annotations
    @native() @HotSpotIntrinsicCandidate()
  23. lazy val hapMap2: VCFInfoHeaderLine
  24. lazy val hapMap3: VCFInfoHeaderLine
  25. def hashCode(): Int
    Definition Classes
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    Annotations
    @native() @HotSpotIntrinsicCandidate()
  26. lazy val infoHeaderLines: Seq[VCFInfoHeaderLine]

    Default set of VCF header lines for INFO fields supported in ADAM.

  27. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  28. lazy val mapq0: VCFFormatHeaderLine
  29. lazy val minReadDepth: VCFFormatHeaderLine
  30. final def ne(arg0: AnyRef): Boolean
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  31. final def notify(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  32. final def notifyAll(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  33. lazy val phaseQuality: VCFFormatHeaderLine
  34. lazy val phaseSetId: VCFFormatHeaderLine
  35. lazy val phredLikelihoods: VCFFormatHeaderLine
  36. lazy val readDepth: VCFInfoHeaderLine
  37. lazy val reverseReadDepth: VCFInfoHeaderLine
  38. lazy val rmsMapq: VCFFormatHeaderLine
  39. lazy val somatic: VCFInfoHeaderLine
  40. lazy val strandBiasComponents: VCFFormatHeaderLine
  41. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  42. lazy val thousandGenomes: VCFInfoHeaderLine
  43. def toString(): String
    Definition Classes
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  44. lazy val transcriptEffects: VCFInfoHeaderLine
  45. lazy val validated: VCFInfoHeaderLine
  46. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  47. final def wait(arg0: Long): Unit
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    @throws( ... ) @native()
  48. final def wait(): Unit
    Definition Classes
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    @throws( ... )

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  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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