Class

com.fulcrumgenomics.umi

FilterConsensusReads

Related Doc: package umi

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class FilterConsensusReads extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
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Inherited
  1. FilterConsensusReads
  2. LazyLogging
  3. FgBioTool
  4. AnyRef
  5. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new FilterConsensusReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, ref: FgBioDef.PathToFasta, reversePerBaseTags: Boolean = false, minReads: Seq[Int], maxReadErrorRate: Seq[Double] = Seq(0.025), maxBaseErrorRate: Seq[Double] = Seq(0.1), minBaseQuality: PhredScore, maxNoCallFraction: Double = 0.2, minMeanBaseQuality: Option[PhredScore] = None, requireSingleStrandAgreement: Boolean = false)

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Type Members

  1. case class FilterResult(keepRead: Boolean, maskedBases: Int) extends Product with Serializable

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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 FilterConsensusReads to any2stringadd[FilterConsensusReads] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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    Implicit information
    This member is added by an implicit conversion from FilterConsensusReads to ArrowAssoc[FilterConsensusReads] 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: (FilterConsensusReads) ⇒ Boolean, msg: ⇒ Any): FilterConsensusReads

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

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

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

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

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

  11. def ensuring(cond: Boolean): FilterConsensusReads

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    Implicit information
    This member is added by an implicit conversion from FilterConsensusReads to Ensuring[FilterConsensusReads] 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. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  14. def execute(): Unit

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    Definition Classes
    FilterConsensusReads → FgBioTool

  15. def fail(exit: Int, message: String): Nothing

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    Fail with a specific error code and message.

    Fail with a specific error code and message.

    Definition Classes
    FgBioTool

  16. def fail(message: String): Nothing

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    Fail with the default exit code and a message.

    Fail with the default exit code and a message.

    Definition Classes
    FgBioTool

  17. def fail(exit: Int): Nothing

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    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool

  18. def finalize(): Unit

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

  19. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  21. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  22. val input: FgBioDef.PathToBam

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  23. def invalid(message: String): Nothing

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    Generates a new validation exception with the given message.

    Generates a new validation exception with the given message.

    Definition Classes
    FgBioTool

  24. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  25. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  26. val maxBaseErrorRate: Seq[Double]

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  27. val maxNoCallFraction: Double

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  28. val maxReadErrorRate: Seq[Double]

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  29. val minBaseQuality: PhredScore

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  30. val minMeanBaseQuality: Option[PhredScore]

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  31. val minReads: Seq[Int]

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

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    Definition Classes
    AnyRef

  33. final def notify(): Unit

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    Definition Classes
    AnyRef

  34. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  35. val output: FgBioDef.PathToBam

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  36. val ref: FgBioDef.PathToFasta

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  37. val requireSingleStrandAgreement: Boolean

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  38. val reversePerBaseTags: Boolean

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

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    Definition Classes
    AnyRef

  40. def toString(): String

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    Definition Classes
    AnyRef → Any

  41. def validate(test: Boolean, message: ⇒ String): Unit

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    Generates a validation exception if the test value is false.

    Generates a validation exception if the test value is false.

    Definition Classes
    FgBioTool

  42. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  45. def →[B](y: B): (FilterConsensusReads, B)

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

Inherited from LazyLogging

Inherited from FgBioTool

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped