org.hammerlab.guacamole.readsets.args

TumorNormalReadsArgs

trait TumorNormalReadsArgs extends Base with ReadFilterArgs

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

Linear Supertypes
Base, NoSequenceDictionaryArgs, ReadFilterArgs, CallLociArgs, AnyRef, Any
Known Subclasses
Arguments
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. TumorNormalReadsArgs
  2. Base
  3. NoSequenceDictionaryArgs
  4. ReadFilterArgs
  5. CallLociArgs
  6. AnyRef
  7. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

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]

    Definition Classes
    Base

  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. var normalReads: String

  26. val normalSampleName: String

  27. final def notify(): Unit

    Definition Classes
    AnyRef

  28. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  29. var onlyMappedReads: Boolean

    Definition Classes
    ReadFilterArgs

  30. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes
    ReadFilterArgs

  31. def paths: Array[String]

    Definition Classes
    TumorNormalReadsArgs → Base

  32. def sampleNames: Array[String]

    Definition Classes
    TumorNormalReadsArgs → Base

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

    Definition Classes
    AnyRef

  34. def toString(): String

    Definition Classes
    AnyRef → Any

  35. var tumorReads: String

  36. val tumorSampleName: String

  37. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  39. 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

Ungrouped