org.hammerlab.guacamole.jointcaller.InputCollection

Arguments

trait Arguments extends Base

Linear Supertypes
Base, NoSequenceDictionaryArgs, ReadFilterArgs, CallLociArgs, AnyRef, Any
Known Subclasses
Arguments
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  1. Arguments
  2. Base
  3. NoSequenceDictionaryArgs
  4. ReadFilterArgs
  5. CallLociArgs
  6. AnyRef
  7. Any
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Abstract Value Members

  1. abstract def paths: Array[String]

    Definition Classes
    Base

  2. abstract def sampleNames: Array[String]

    Definition Classes
    Base

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. var analytes: Array[String]

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  14. var includeDuplicates: Boolean

    Definition Classes
    ReadFilterArgs

  15. var includeFailedQualityChecks: Boolean

    Definition Classes
    ReadFilterArgs

  16. var includeSingleEnd: Boolean

    Definition Classes
    ReadFilterArgs

  17. lazy val inputs: PerSample[readsets.io.Input]

    Definition Classes
    Base

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  19. var lociFile: String

    Attributes
    protected
    Definition Classes
    CallLociArgs

  20. def lociFileOpt: Option[String]

    Definition Classes
    CallLociArgs

  21. var lociStr: String

    Attributes
    protected
    Definition Classes
    CallLociArgs

  22. def lociStrOpt: Option[String]

    Definition Classes
    CallLociArgs

  23. var minAlignmentQuality: Int

    Definition Classes
    ReadFilterArgs

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

    Definition Classes
    AnyRef

  25. var noSequenceDictionary: Boolean

    Definition Classes
    NoSequenceDictionaryArgs

  26. final def notify(): Unit

    Definition Classes
    AnyRef

  27. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  28. var onlyMappedReads: Boolean

    Definition Classes
    ReadFilterArgs

  29. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes
    ReadFilterArgs

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

    Definition Classes
    AnyRef

  31. var tissueTypes: Array[String]

  32. def toString(): String

    Definition Classes
    AnyRef → Any

  33. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Base

Inherited from NoSequenceDictionaryArgs

Inherited from ReadFilterArgs

Inherited from CallLociArgs

Inherited from AnyRef

Inherited from Any

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