org.hammerlab.guacamole.readsets.args

Base

trait Base extends ReadFilterArgs with NoSequenceDictionaryArgs

Linear Supertypes
NoSequenceDictionaryArgs, ReadFilterArgs, CallLociArgs, AnyRef, Any
Known Subclasses
Arguments, Arguments, Arguments, Arguments, Arguments, Arguments, Arguments, GermlineCallerArgs, PartitionLociArgs, PartitionReadsArgs, SingleSampleArgs, TumorNormalReadsArgs
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Inherited
  1. Base
  2. NoSequenceDictionaryArgs
  3. ReadFilterArgs
  4. CallLociArgs
  5. AnyRef
  6. Any
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Abstract Value Members

  1. abstract def paths: Array[String]

  2. abstract def sampleNames: Array[String]

Concrete 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. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  10. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  12. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  13. var includeDuplicates: Boolean

    Definition Classes
    ReadFilterArgs

  14. var includeFailedQualityChecks: Boolean

    Definition Classes
    ReadFilterArgs

  15. var includeSingleEnd: Boolean

    Definition Classes
    ReadFilterArgs

  16. lazy val inputs: PerSample[Input]

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  18. var lociFile: String

    Attributes
    protected
    Definition Classes
    CallLociArgs

  19. def lociFileOpt: Option[String]

    Definition Classes
    CallLociArgs

  20. var lociStr: String

    Attributes
    protected
    Definition Classes
    CallLociArgs

  21. def lociStrOpt: Option[String]

    Definition Classes
    CallLociArgs

  22. var minAlignmentQuality: Int

    Definition Classes
    ReadFilterArgs

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

    Definition Classes
    AnyRef

  24. var noSequenceDictionary: Boolean

    Definition Classes
    NoSequenceDictionaryArgs

  25. final def notify(): Unit

    Definition Classes
    AnyRef

  26. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  27. var onlyMappedReads: Boolean

    Definition Classes
    ReadFilterArgs

  28. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes
    ReadFilterArgs

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

    Definition Classes
    AnyRef

  30. def toString(): String

    Definition Classes
    AnyRef → Any

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from NoSequenceDictionaryArgs

Inherited from ReadFilterArgs

Inherited from CallLociArgs

Inherited from AnyRef

Inherited from Any

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