org.hammerlab.guacamole.jointcaller

Input

case class Input(index: SampleId, sampleName: SampleName, path: String, tissueType: Input.TissueType.Value, analyte: Input.Analyte.Value) extends readsets.io.Input with Product with Serializable

An input BAM to the joint variant caller.

The caller can work with any number of normal and tumor BAMs, each of which may be DNA or RNA.

index

Throughout the joint caller, we refer to inputs by index, which is the index (0 <= index < num inputs) of the input as specified on the commandline

sampleName

arbitrary name for this sample, used in VCF output

path

path to BAM

tissueType

tumor or normal

analyte

rna or dna

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Product, Equals, readsets.io.Input, Serializable, Serializable, AnyRef, Any
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Instance Constructors

  1. new Input(index: SampleId, sampleName: SampleName, path: String, tissueType: Input.TissueType.Value, analyte: Input.Analyte.Value)

    index

    Throughout the joint caller, we refer to inputs by index, which is the index (0 <= index < num inputs) of the input as specified on the commandline

    sampleName

    arbitrary name for this sample, used in VCF output

    path

    path to BAM

    tissueType

    tumor or normal

    analyte

    rna or dna

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. val analyte: Input.Analyte.Value

    rna or dna

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

  9. def dna: Boolean

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

    Definition Classes
    AnyRef

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. val id: SampleId

    Definition Classes
    Input

  14. val index: SampleId

    Throughout the joint caller, we refer to inputs by index, which is the index (0 <= index < num inputs) of the input as specified on the commandline

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  17. def normal: Boolean

  18. def normalDNA: Boolean

  19. def normalRNA: Boolean

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. val path: String

    path to BAM

    path to BAM

    Definition Classes
    Input → Input

  23. def rna: Boolean

  24. val sampleName: SampleName

    arbitrary name for this sample, used in VCF output

    arbitrary name for this sample, used in VCF output

    Definition Classes
    Input → Input

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

    Definition Classes
    AnyRef

  26. val tissueType: Input.TissueType.Value

    tumor or normal

  27. def toString(): String

    Definition Classes
    Input → AnyRef → Any

  28. def tumor: Boolean

  29. def tumorDNA: Boolean

  30. def tumorRNA: Boolean

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from readsets.io.Input

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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