Class/Object

com.fulcrumgenomics.umi

CorrectUmis

Related Docs: object CorrectUmis | package umi

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class CorrectUmis extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. CorrectUmis
  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 CorrectUmis(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, rejects: Option[FgBioDef.PathToBam] = None, metrics: Option[FgBioDef.FilePath] = None, maxMismatches: Int, minDistance: Int, umis: Seq[String] = Seq.empty, umiFiles: Seq[FgBioDef.FilePath] = Seq.empty, umiTag: String = ConsensusTags.UmiBases, dontStoreOriginalUmis: Boolean = false)

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

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

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    Implicit information
    This member is added by an implicit conversion from CorrectUmis to ArrowAssoc[CorrectUmis] 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. val dontStoreOriginalUmis: Boolean

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  9. def ensuring(cond: (CorrectUmis) ⇒ Boolean, msg: ⇒ Any): CorrectUmis

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

  10. def ensuring(cond: (CorrectUmis) ⇒ Boolean): CorrectUmis

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

  11. def ensuring(cond: Boolean, msg: ⇒ Any): CorrectUmis

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

  12. def ensuring(cond: Boolean): CorrectUmis

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

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

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    Definition Classes
    AnyRef

  14. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  15. def execute(): Unit

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    Definition Classes
    CorrectUmis → FgBioTool

  16. 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

  17. 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

  18. def fail(exit: Int): Nothing

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    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool

  19. def finalize(): Unit

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

  20. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  22. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  23. val input: FgBioDef.PathToBam

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  24. 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

  25. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  26. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  27. val maxMismatches: Int

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  28. val metrics: Option[FgBioDef.FilePath]

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  29. val minDistance: Int

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

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    Definition Classes
    AnyRef

  31. final def notify(): Unit

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    Definition Classes
    AnyRef

  32. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  33. val output: FgBioDef.PathToBam

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  34. val rejects: Option[FgBioDef.PathToBam]

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

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    Definition Classes
    AnyRef

  36. def toString(): String

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    Definition Classes
    AnyRef → Any

  37. val umiFiles: Seq[FgBioDef.FilePath]

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  38. val umiTag: String

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  39. val umis: Seq[String]

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  40. 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

  41. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  44. def →[B](y: B): (CorrectUmis, B)

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    Implicit information
    This member is added by an implicit conversion from CorrectUmis to ArrowAssoc[CorrectUmis] 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 CorrectUmis to any2stringadd[CorrectUmis]

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

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

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

Ungrouped