org.bdgenomics.avocado.cli

BiallelicGenotyperArgs

class BiallelicGenotyperArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs with PrefilterReadsArgs with HardFilterGenotypesArgs with RewriteHetsArgs

Linear Supertypes
RewriteHetsArgs, HardFilterGenotypesArgs, PrefilterReadsArgs, Serializable, Serializable, ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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Inherited
  1. BiallelicGenotyperArgs
  2. RewriteHetsArgs
  3. HardFilterGenotypesArgs
  4. PrefilterReadsArgs
  5. Serializable
  6. Serializable
  7. ParquetArgs
  8. ADAMSaveAnyArgs
  9. SaveArgs
  10. ParquetRDDArgs
  11. Args4jBase
  12. AnyRef
  13. Any
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Instance Constructors

  1. new BiallelicGenotyperArgs()

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. var asSingleFile: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

  8. var autosomalOnly: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  9. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  10. def clone(): AnyRef

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

  11. var cnvCalls: String

  12. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  13. var deferMerging: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

  14. var desiredMaxCoverage: Int

  15. var desiredPartitionCount: Int

  16. var desiredPartitionSize: Int

  17. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  18. var disableFastConcat: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

  19. var disableHetIndelRewriting: Boolean

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs

  20. var disableHetSnpRewriting: Boolean

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs

  21. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase

  22. var emitAllGenotypes: Boolean

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

    Definition Classes
    AnyRef

  24. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  25. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  27. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  28. var inputPath: String

  29. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  30. var isNotGrc: Boolean

  31. var keepDuplicates: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  32. var keepMitochondrialChromosome: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  33. var keepNonPrimary: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  34. var logLevel: String

    Definition Classes
    ParquetArgs

  35. var maxHetIndelAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs → HardFilterGenotypesArgs

  36. var maxHetSnpAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs → HardFilterGenotypesArgs

  37. var maxIndelDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  38. var maxIndelPhredStrandBias: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  39. var maxSnpDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  40. var maxSnpPhredStrandBias: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  41. var minHetIndelAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  42. var minHetIndelQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  43. var minHetSnpAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  44. var minHetSnpQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  45. var minHomIndelAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  46. var minHomIndelQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  47. var minHomSnpAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  48. var minHomSnpQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  49. var minIndelDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  50. var minIndelRMSMappingQuality: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  51. var minMappingQuality: Int

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  52. var minObservationsForDiscovery: Int

  53. var minPhredForDiscovery: Int

  54. var minQuality: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  55. var minSnpDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  56. var minSnpRMSMappingQuality: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

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

    Definition Classes
    AnyRef

  58. final def notify(): Unit

    Definition Classes
    AnyRef

  59. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  60. var outputPath: String

    Definition Classes
    BiallelicGenotyperArgs → SaveArgs

  61. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  62. var ploidy: Int

  63. var printMetrics: Boolean

    Definition Classes
    Args4jBase

  64. var scoreAllSites: Boolean

  65. var sortFastqOutput: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

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

    Definition Classes
    AnyRef

  67. def toString(): String

    Definition Classes
    AnyRef → Any

  68. var variantsToCall: String

  69. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from RewriteHetsArgs

Inherited from HardFilterGenotypesArgs

Inherited from PrefilterReadsArgs

Inherited from Serializable

Inherited from Serializable

Inherited from ParquetArgs

Inherited from ADAMSaveAnyArgs

Inherited from SaveArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

Ungrouped