Trait

org.hammerlab.genomics.readsets.args

Base

Related Doc: package args

Permalink

trait Base extends ReadFilterArgs with NoSequenceDictionaryArgs

Linear Supertypes
NoSequenceDictionaryArgs, ReadFilterArgs, LociArgs, AnyRef, Any
Known Subclasses
Arguments, SingleSampleArgs, TumorNormalReadsArgs
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. Base
  2. NoSequenceDictionaryArgs
  3. ReadFilterArgs
  4. LociArgs
  5. AnyRef
  6. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract def paths: Array[String]

    Permalink

  2. abstract def sampleNames: Array[String]

    Permalink

Concrete Value Members

  1. final def !=(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

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

    Permalink
    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

  5. def clone(): AnyRef

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

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

    Permalink
    Definition Classes
    AnyRef

  7. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  8. def finalize(): Unit

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

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

    Permalink
    Definition Classes
    AnyRef → Any

  10. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  11. var includeDuplicates: Boolean

    Permalink
    Definition Classes
    ReadFilterArgs

  12. var includeFailedQualityChecks: Boolean

    Permalink
    Definition Classes
    ReadFilterArgs

  13. var includeSingleEnd: Boolean

    Permalink
    Definition Classes
    ReadFilterArgs

  14. lazy val inputs: PerSample[Input]

    Permalink

  15. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any

  16. var lociFileOpt: Option[String]

    Permalink
    Definition Classes
    LociArgs

  17. var lociStrOpt: Option[String]

    Permalink
    Definition Classes
    LociArgs

  18. var minAlignmentQualityOpt: Option[Int]

    Permalink
    Definition Classes
    ReadFilterArgs

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

    Permalink
    Definition Classes
    AnyRef

  20. var noSequenceDictionary: Boolean

    Permalink
    Definition Classes
    NoSequenceDictionaryArgs

  21. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  22. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  23. var onlyMappedReads: Boolean

    Permalink
    Definition Classes
    ReadFilterArgs

  24. def parseConfig(hadoopConfiguration: Configuration): InputConfig

    Permalink
    Definition Classes
    ReadFilterArgs

  25. var splitSize: Option[String]

    Permalink
    Definition Classes
    ReadFilterArgs

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

    Permalink
    Definition Classes
    AnyRef

  27. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any

  28. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from NoSequenceDictionaryArgs

Inherited from ReadFilterArgs

Inherited from LociArgs

Inherited from AnyRef

Inherited from Any

Ungrouped