Trait

org.hammerlab.genomics.readsets.args

TumorNormalReadsArgs

Related Doc: package args

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trait TumorNormalReadsArgs extends Base with ReadFilterArgs

Arguments for accepting two sets of reads (tumor + normal).

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Base, NoSequenceDictionaryArgs, ReadFilterArgs, LociArgs, AnyRef, Any
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  1. TumorNormalReadsArgs
  2. Base
  3. NoSequenceDictionaryArgs
  4. ReadFilterArgs
  5. LociArgs
  6. AnyRef
  7. Any
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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 clone(): AnyRef

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

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

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    Definition Classes
    AnyRef

  7. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  8. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  10. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  11. var includeDuplicates: Boolean

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    Definition Classes
    ReadFilterArgs

  12. var includeFailedQualityChecks: Boolean

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    Definition Classes
    ReadFilterArgs

  13. var includeSingleEnd: Boolean

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    Definition Classes
    ReadFilterArgs

  14. lazy val inputs: PerSample[Input]

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    Definition Classes
    Base

  15. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  16. var lociFileOpt: Option[String]

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    Definition Classes
    LociArgs

  17. var lociStrOpt: Option[String]

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    Definition Classes
    LociArgs

  18. var minAlignmentQualityOpt: Option[Int]

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    Definition Classes
    ReadFilterArgs

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

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    Definition Classes
    AnyRef

  20. var noSequenceDictionary: Boolean

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    Definition Classes
    NoSequenceDictionaryArgs

  21. var normalReads: String

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  22. val normalSampleName: String

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  23. final def notify(): Unit

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    Definition Classes
    AnyRef

  24. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  25. var onlyMappedReads: Boolean

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    Definition Classes
    ReadFilterArgs

  26. def parseConfig(hadoopConfiguration: Configuration): InputConfig

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    Definition Classes
    ReadFilterArgs

  27. def paths: Array[String]

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    Definition Classes
    TumorNormalReadsArgs → Base

  28. def sampleNames: Array[String]

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    Definition Classes
    TumorNormalReadsArgs → Base

  29. var splitSize: Option[String]

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    Definition Classes
    ReadFilterArgs

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

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    Definition Classes
    AnyRef

  31. def toString(): String

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    AnyRef → Any

  32. var tumorReads: String

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  33. val tumorSampleName: String

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  34. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    AnyRef
    Annotations
    @throws( ... )

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

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    @throws( ... )

Inherited from Base

Inherited from NoSequenceDictionaryArgs

Inherited from ReadFilterArgs

Inherited from LociArgs

Inherited from AnyRef

Inherited from Any

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