org.hammerlab.guacamole.readsets.args

Arguments

trait Arguments extends Base

Common command-line arguments for loading in one or more sets of reads, and associating a sample-name with each.

Linear Supertypes
Base, NoSequenceDictionaryArgs, ReadFilterArgs, CallLociArgs, AnyRef, Any
Known Subclasses
Arguments, Arguments, Arguments, PartitionLociArgs, PartitionReadsArgs
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Inherited
  1. Arguments
  2. Base
  3. NoSequenceDictionaryArgs
  4. ReadFilterArgs
  5. CallLociArgs
  6. AnyRef
  7. Any
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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. final def notify(): Unit

    Definition Classes
    AnyRef

  26. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  27. var onlyMappedReads: Boolean

    Definition Classes
    ReadFilterArgs

  28. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes
    ReadFilterArgs

  29. var paths: Array[String]

    Definition Classes
    Arguments → Base

  30. var sampleNames: Array[String]

    Definition Classes
    Arguments → Base

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

    Definition Classes
    AnyRef

  32. def toString(): String

    Definition Classes
    AnyRef → Any

  33. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  35. 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

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