Trait

org.hammerlab.genomics.readsets.args.impl

PrefixedSingleSampleArgs

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trait PrefixedSingleSampleArgs extends SingleSampleArgsI with PrefixedPathsBase

SingleSampleArgsI implementation that supports path-prefixing.

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

  1. implicit abstract def pathPrefixOpt: Option[PathPrefix]

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    Attributes
    protected
    Definition Classes
    PrefixedPathsBase

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 paths: Array[Path]

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    Definition Classes
    PrefixedPathsBase → InputArgs

  26. var reads: UnprefixedPath

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  27. def sampleName: String

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    Definition Classes
    SingleSampleArgsI

  28. def sampleNames: Array[String]

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    Definition Classes
    SingleSampleArgsI → InputArgs

  29. var splitSizeOpt: Option[Bytes]

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    Definition Classes
    ReadFilterArgs → ReadFilters

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

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    Definition Classes
    AnyRef

  31. def toString(): String

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    Definition Classes
    AnyRef → Any

  32. def unprefixedPaths: Array[UnprefixedPath]

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    Attributes
    protected
    Definition Classes
    PrefixedSingleSampleArgs → PrefixedPathsBase

  33. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from PrefixedPathsBase

Inherited from SingleSampleArgsI

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