Class

com.fulcrumgenomics.bam

UpdateReadGroups

Related Doc: package bam

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class UpdateReadGroups extends FgBioTool with LazyLogging

Updates one or more read groups.

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
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Inherited
  1. UpdateReadGroups
  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 UpdateReadGroups(input: dagr.commons.CommonsDef.PathToBam, output: dagr.commons.CommonsDef.PathToBam, readGroupsFile: dagr.commons.CommonsDef.PathToBam, keepReadGroupAttributes: Boolean = false, ignoreMissingReadGroups: 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 UpdateReadGroups to any2stringadd[UpdateReadGroups] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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

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

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

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

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

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

  11. def ensuring(cond: Boolean): UpdateReadGroups

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    Implicit information
    This member is added by an implicit conversion from UpdateReadGroups to Ensuring[UpdateReadGroups] 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
    UpdateReadGroups → 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 UpdateReadGroups to StringFormat[UpdateReadGroups] 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 ignoreMissingReadGroups: Boolean

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  23. val input: dagr.commons.CommonsDef.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. val keepReadGroupAttributes: Boolean

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  27. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

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

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    Definition Classes
    AnyRef

  29. final def notify(): Unit

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    Definition Classes
    AnyRef

  30. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  31. val output: dagr.commons.CommonsDef.PathToBam

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  32. val readGroupsFile: dagr.commons.CommonsDef.PathToBam

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

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    Definition Classes
    AnyRef

  34. def toString(): String

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    Definition Classes
    AnyRef → Any

  35. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  38. def →[B](y: B): (UpdateReadGroups, B)

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

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

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

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

Ungrouped