Trait

org.hammerlab.genomics.readsets.args.base

Base

Related Doc: package base

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trait Base extends ReadFilters with InputArgs

Linear Supertypes
InputArgs, ReadFilters, LociInput, AnyRef, Any
Known Subclasses
Arguments, PathPrefixArg, PathsArgs, PrefixedPathsBase, PrefixedSingleSampleArgs, SingleSampleArgs, SingleSampleArgsI
Ordering
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  2. By Inheritance
Inherited
  1. Base
  2. InputArgs
  3. ReadFilters
  4. LociInput
  5. AnyRef
  6. Any
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Visibility
  1. Public
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Abstract Value Members

  1. abstract def includeDuplicates: Boolean

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    Definition Classes
    ReadFilters

  2. abstract def includeFailedQualityChecks: Boolean

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    Definition Classes
    ReadFilters

  3. abstract def includeSingleEnd: Boolean

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    Definition Classes
    ReadFilters

  4. abstract def lociFileOpt: Option[Path]

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    Definition Classes
    LociInput

  5. abstract def lociStrOpt: Option[String]

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    Definition Classes
    LociInput

  6. abstract def minAlignmentQualityOpt: Option[Int]

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    Definition Classes
    ReadFilters

  7. abstract def noSequenceDictionary: Boolean

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  8. abstract def onlyMappedReads: Boolean

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    Definition Classes
    ReadFilters

  9. abstract def paths: Array[Path]

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    Definition Classes
    InputArgs

  10. abstract def sampleNames: Array[Name]

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    Definition Classes
    InputArgs

  11. abstract def splitSizeOpt: Option[Bytes]

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    Definition Classes
    ReadFilters

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. lazy val inputs: Inputs

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    Definition Classes
    InputArgs

  12. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  14. final def notify(): Unit

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    Definition Classes
    AnyRef

  15. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    ReadFilters

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

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    Definition Classes
    AnyRef

  18. def toString(): String

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    Definition Classes
    AnyRef → Any

  19. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from InputArgs

Inherited from ReadFilters

Inherited from LociInput

Inherited from AnyRef

Inherited from Any

Ungrouped