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
Ordering
  1. Alphabetic
  2. By Inheritance
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
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

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)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    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)
    Implicit
    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
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  8. def ensuring(cond: (VanillaUmiConsensusCallerOptions) ⇒ Boolean, msg: ⇒ Any): VanillaUmiConsensusCallerOptions
    Implicit
    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
    Implicit
    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
    Implicit
    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
    Implicit
    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
    Definition Classes
    AnyRef
  13. val errorRatePostUmi: PhredScore
  14. val errorRatePreUmi: PhredScore
  15. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    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[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. val maxReads: Int
  20. val minConsensusBaseQuality: PhredScore
  21. val minInputBaseQuality: PhredScore
  22. val minReads: Int
  23. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  25. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  26. val producePerBaseTags: Boolean
  27. val qualityTrim: Boolean
  28. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  29. val tag: String
  30. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  33. def →[B](y: B): (VanillaUmiConsensusCallerOptions, B)
    Implicit
    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