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: Any): Boolean

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  5. var asSingleFile: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

  6. var autosomalOnly: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  7. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  8. def clone(): AnyRef

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

  9. var cnvCalls: String

  10. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  11. var deferMerging: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

  12. var desiredMaxCoverage: Int

  13. var desiredPartitionCount: Int

  14. var desiredPartitionSize: Int

  15. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  16. var disableFastConcat: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

  17. var disableHetIndelRewriting: Boolean

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs

  18. var disableHetSnpRewriting: Boolean

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs

  19. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase

  20. var emitAllGenotypes: Boolean

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

    Definition Classes
    AnyRef

  22. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  23. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  25. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  26. var inputPath: String

  27. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  28. var isNotGrc: Boolean

  29. var keepDuplicates: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  30. var keepMitochondrialChromosome: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  31. var keepNonPrimary: Boolean

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  32. var logLevel: String

    Definition Classes
    ParquetArgs

  33. var maxHetIndelAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs → HardFilterGenotypesArgs

  34. var maxHetSnpAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → RewriteHetsArgs → HardFilterGenotypesArgs

  35. var maxIndelDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  36. var maxIndelPhredStrandBias: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  37. var maxSnpDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  38. var maxSnpPhredStrandBias: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  39. var minHetIndelAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  40. var minHetIndelQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  41. var minHetSnpAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  42. var minHetSnpQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  43. var minHomIndelAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  44. var minHomIndelQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  45. var minHomSnpAltAllelicFraction: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  46. var minHomSnpQualityByDepth: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  47. var minIndelDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  48. var minIndelRMSMappingQuality: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  49. var minMappingQuality: Int

    Definition Classes
    BiallelicGenotyperArgs → PrefilterReadsArgs

  50. var minObservationsForDiscovery: Int

  51. var minPhredForDiscovery: Int

  52. var minQuality: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  53. var minSnpDepth: Int

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

  54. var minSnpRMSMappingQuality: Float

    Definition Classes
    BiallelicGenotyperArgs → HardFilterGenotypesArgs

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

    Definition Classes
    AnyRef

  56. final def notify(): Unit

    Definition Classes
    AnyRef

  57. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  58. var outputPath: String

    Definition Classes
    BiallelicGenotyperArgs → SaveArgs

  59. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  60. var ploidy: Int

  61. var printMetrics: Boolean

    Definition Classes
    Args4jBase

  62. var scoreAllSites: Boolean

  63. var sortFastqOutput: Boolean

    Definition Classes
    BiallelicGenotyperArgs → ADAMSaveAnyArgs

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

    Definition Classes
    AnyRef

  65. def toString(): String

    Definition Classes
    AnyRef → Any

  66. var variantsToCall: String

  67. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  69. 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