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 AnnotateBamWithUmis to any2stringadd[AnnotateBamWithUmis] performed by method any2stringadd in scala.Predef.

   Definition Classes

   any2stringadd

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

   Implicit

   This member is added by an implicit conversion from AnnotateBamWithUmis to ArrowAssoc[AnnotateBamWithUmis] 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.  val attribute: String
8.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   Implicit

   This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.

   Definition Classes

   Ensuring

10.  def ensuring(cond: (AnnotateBamWithUmis) ⇒ Boolean): AnnotateBamWithUmis

    Implicit

    This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

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

    Implicit

    This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

12.  def ensuring(cond: Boolean): AnnotateBamWithUmis

    Implicit

    This member is added by an implicit conversion from AnnotateBamWithUmis to Ensuring[AnnotateBamWithUmis] 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

    Main method that does the work of reading input files, matching up reads and writing the output file.

    Main method that does the work of reading input files, matching up reads and writing the output file.

    Definition Classes

    AnnotateBamWithUmis → 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.  val failFast: Boolean
20.  val fastq: FgBioDef.PathToFastq
21.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

22.  def formatted(fmtstr: String): String

    Implicit

    This member is added by an implicit conversion from AnnotateBamWithUmis to StringFormat[AnnotateBamWithUmis] performed by method StringFormat in scala.Predef.

    Definition Classes

    StringFormat

    Annotations

    @inline()

23.  final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

24.  def hashCode(): Int

    Definition Classes

    AnyRef → Any

25.  val input: FgBioDef.PathToBam
26.  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

27.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

28.  lazy val logger: Logger

    Attributes

    protected

    Definition Classes

    LazyLogging

29.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

30.  final def notify(): Unit

    Definition Classes

    AnyRef

31.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

32.  val output: FgBioDef.PathToBam
33.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

34.  def toString(): String

    Definition Classes

    AnyRef → Any

35.  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

36.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

38.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

39.  def →[B](y: B): (AnnotateBamWithUmis, B)

    Implicit

    This member is added by an implicit conversion from AnnotateBamWithUmis to ArrowAssoc[AnnotateBamWithUmis] performed by method ArrowAssoc in scala.Predef.

    Definition Classes

    ArrowAssoc