Trait

org.hammerlab.genomics.readsets.args.impl

SingleSampleArgsI

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trait SingleSampleArgsI extends Base with NoSequenceDictionaryArgs with ReadFilterArgs

Argument for accepting a single set of reads (for e.g. germline variant calling).

Linear Supertypes
ReadFilterArgs, LociArgs, NoSequenceDictionaryArgs, Base, InputArgs, ReadFilters, LociInput, AnyRef, Any
Known Subclasses
PrefixedSingleSampleArgs, SingleSampleArgs
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Inherited
  1. SingleSampleArgsI
  2. ReadFilterArgs
  3. LociArgs
  4. NoSequenceDictionaryArgs
  5. Base
  6. InputArgs
  7. ReadFilters
  8. LociInput
  9. AnyRef
  10. Any
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Visibility
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Abstract Value Members

  1. abstract def paths: Array[Path]

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    Definition Classes
    InputArgs

Concrete 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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    Attributes
    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 → ReadFilters

  12. var includeFailedQualityChecks: Boolean

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    Definition Classes
    ReadFilterArgs → ReadFilters

  13. var includeSingleEnd: Boolean

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    Definition Classes
    ReadFilterArgs → ReadFilters

  14. lazy val inputs: Inputs

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    Definition Classes
    InputArgs

  15. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  16. var lociFileOpt: Option[Path]

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    Definition Classes
    LociArgs → LociInput

  17. var lociStrOpt: Option[String]

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    Definition Classes
    LociArgs → LociInput

  18. var minAlignmentQualityOpt: Option[Int]

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    Definition Classes
    ReadFilterArgs → ReadFilters

  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. final def notify(): Unit

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    Definition Classes
    AnyRef

  22. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  23. var onlyMappedReads: Boolean

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    Definition Classes
    ReadFilterArgs → ReadFilters

  24. def parseConfig(implicit conf: Configuration): Config

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    Definition Classes
    ReadFilters

  25. def sampleName: String

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  26. def sampleNames: Array[String]

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    Definition Classes
    SingleSampleArgsI → InputArgs

  27. var splitSizeOpt: Option[Bytes]

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    Definition Classes
    ReadFilterArgs → ReadFilters

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

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    Definition Classes
    AnyRef

  29. def toString(): String

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    Definition Classes
    AnyRef → Any

  30. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ReadFilterArgs

Inherited from LociArgs

Inherited from NoSequenceDictionaryArgs

Inherited from Base

Inherited from InputArgs

Inherited from ReadFilters

Inherited from LociInput

Inherited from AnyRef

Inherited from Any

Ungrouped