Class/Object

com.fulcrumgenomics.umi

VanillaUmiConsensusCallerOptions

Related Docs: object VanillaUmiConsensusCallerOptions | package umi

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case class VanillaUmiConsensusCallerOptions(tag: String = DefaultTag, errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality, qualityTrim: Boolean = DefaultQualityTrim, minConsensusBaseQuality: PhredScore = DefaultMinConsensusBaseQuality, minReads: Int = DefaultMinReads, maxReads: Int = DefaultMaxReads, producePerBaseTags: Boolean = DefaultProducePerBaseTags) extends Product with Serializable

Holds the parameters/options for consensus calling.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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Inherited
  1. VanillaUmiConsensusCallerOptions
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. AnyRef
  7. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
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Instance Constructors

  1. new VanillaUmiConsensusCallerOptions(tag: String = DefaultTag, errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality, qualityTrim: Boolean = DefaultQualityTrim, minConsensusBaseQuality: PhredScore = DefaultMinConsensusBaseQuality, minReads: Int = DefaultMinReads, maxReads: Int = DefaultMaxReads, producePerBaseTags: Boolean = DefaultProducePerBaseTags)

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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. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to any2stringadd[VanillaUmiConsensusCallerOptions] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  4. def ->[B](y: B): (VanillaUmiConsensusCallerOptions, B)

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to ArrowAssoc[VanillaUmiConsensusCallerOptions] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

  5. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. def ensuring(cond: (VanillaUmiConsensusCallerOptions) ⇒ Boolean, msg: ⇒ Any): VanillaUmiConsensusCallerOptions

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to Ensuring[VanillaUmiConsensusCallerOptions] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  9. def ensuring(cond: (VanillaUmiConsensusCallerOptions) ⇒ Boolean): VanillaUmiConsensusCallerOptions

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to Ensuring[VanillaUmiConsensusCallerOptions] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  10. def ensuring(cond: Boolean, msg: ⇒ Any): VanillaUmiConsensusCallerOptions

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to Ensuring[VanillaUmiConsensusCallerOptions] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  11. def ensuring(cond: Boolean): VanillaUmiConsensusCallerOptions

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to Ensuring[VanillaUmiConsensusCallerOptions] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  13. val errorRatePostUmi: PhredScore

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  14. val errorRatePreUmi: PhredScore

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  15. def finalize(): Unit

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

  16. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to StringFormat[VanillaUmiConsensusCallerOptions] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

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

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    Definition Classes
    AnyRef → Any

  18. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  19. val maxReads: Int

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  20. val minConsensusBaseQuality: PhredScore

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  21. val minInputBaseQuality: PhredScore

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  22. val minReads: Int

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

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    Definition Classes
    AnyRef

  24. final def notify(): Unit

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    Definition Classes
    AnyRef

  25. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  26. val producePerBaseTags: Boolean

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  27. val qualityTrim: Boolean

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

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    Definition Classes
    AnyRef

  29. val tag: String

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  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( ... )

  33. def →[B](y: B): (VanillaUmiConsensusCallerOptions, B)

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    Implicit information
    This member is added by an implicit conversion from VanillaUmiConsensusCallerOptions to ArrowAssoc[VanillaUmiConsensusCallerOptions] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from VanillaUmiConsensusCallerOptions to any2stringadd[VanillaUmiConsensusCallerOptions]

Inherited by implicit conversion StringFormat from VanillaUmiConsensusCallerOptions to StringFormat[VanillaUmiConsensusCallerOptions]

Inherited by implicit conversion Ensuring from VanillaUmiConsensusCallerOptions to Ensuring[VanillaUmiConsensusCallerOptions]

Inherited by implicit conversion ArrowAssoc from VanillaUmiConsensusCallerOptions to ArrowAssoc[VanillaUmiConsensusCallerOptions]

Ungrouped