c

com.fulcrumgenomics.bam

SetMateInformation

class SetMateInformation extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SetMateInformation
  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 SetMateInformation(input: FgBioDef.PathToBam = Io.StdIn, output: FgBioDef.PathToBam = Io.StdOut, ref: Option[FgBioDef.PathToFasta] = None, allowMissingMates: Boolean = false)

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 SetMateInformation to any2stringadd[SetMateInformation] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (SetMateInformation, B)
    Implicit
    This member is added by an implicit conversion from SetMateInformation to ArrowAssoc[SetMateInformation] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. val allowMissingMates: Boolean
  7. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  8. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. def ensuring(cond: (SetMateInformation) ⇒ Boolean, msg: ⇒ Any): SetMateInformation
    Implicit
    This member is added by an implicit conversion from SetMateInformation to Ensuring[SetMateInformation] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (SetMateInformation) ⇒ Boolean): SetMateInformation
    Implicit
    This member is added by an implicit conversion from SetMateInformation to Ensuring[SetMateInformation] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): SetMateInformation
    Implicit
    This member is added by an implicit conversion from SetMateInformation to Ensuring[SetMateInformation] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): SetMateInformation
    Implicit
    This member is added by an implicit conversion from SetMateInformation to Ensuring[SetMateInformation] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  15. def execute(): Unit
    Definition Classes
    SetMateInformation → FgBioTool
  16. def fail(exit: Int, message: String): Nothing

    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

    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

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool
  19. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  20. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from SetMateInformation to StringFormat[SetMateInformation] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  21. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  22. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  23. val input: FgBioDef.PathToBam
  24. def invalid(message: String): Nothing

    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
    Definition Classes
    Any
  26. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. final def notify(): Unit
    Definition Classes
    AnyRef
  29. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  30. val output: FgBioDef.PathToBam
  31. val ref: Option[FgBioDef.PathToFasta]
  32. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  33. def toString(): String
    Definition Classes
    AnyRef → Any
  34. def validate(test: Boolean, message: ⇒ String): Unit

    Generates a validation exception if the test value is false.

    Generates a validation exception if the test value is false.

    Definition Classes
    FgBioTool
  35. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  36. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. def →[B](y: B): (SetMateInformation, B)
    Implicit
    This member is added by an implicit conversion from SetMateInformation to ArrowAssoc[SetMateInformation] 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 SetMateInformation to any2stringadd[SetMateInformation]

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

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

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

Ungrouped