Packages

object FgBioDef extends CommonsDef

FgBioDef that is just an extension of the commons CommonsDef. Here in case there's a need for FgBio specific defs later.

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Type Members

  1. implicit class BetterBufferedIteratorJavaWrapper[A] extends AnyRef
    Definition Classes
    CommonsDef
  2. implicit class BetterBufferedIteratorScalaWrapper[A] extends AnyRef
    Definition Classes
    CommonsDef
  3. type DirPath = Path
    Definition Classes
    CommonsDef
  4. trait DualIterator[A] extends Iterator[A] with Iterator[A]
    Definition Classes
    CommonsDef
  5. trait FgBioEnum [T <: EnumEntry] extends Enum[T]

    Extends this trait in your enumeration object to enable the case objects to be created on the command line.

    Extends this trait in your enumeration object to enable the case objects to be created on the command line. You should implement the Enum#values method in your object, for example: def values: IndexedSeq[T] = findValues.

  6. type FilePath = Path
    Definition Classes
    CommonsDef
  7. type FilenamePrefix = String
    Definition Classes
    CommonsDef
  8. implicit class IteratorToJavaCollectionsAdapter[A] extends AnyRef
    Definition Classes
    CommonsDef
  9. implicit class ParSupport[A, B <: ParIterableLike[_, _, _]] extends AnyRef
    Definition Classes
    CommonsDef
  10. type PathPrefix = Path
    Definition Classes
    CommonsDef
  11. type PathToBam = Path
    Definition Classes
    CommonsDef
  12. type PathToFasta = Path
    Definition Classes
    CommonsDef
  13. type PathToFastq = Path
    Definition Classes
    CommonsDef
  14. type PathToIntervals = Path
    Definition Classes
    CommonsDef
  15. type PathToVcf = Path
    Definition Classes
    CommonsDef
  16. implicit class SafelyClosable extends AnyRef
    Definition Classes
    CommonsDef
  17. implicit class SumBy[A] extends AnyRef
    Definition Classes
    CommonsDef

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. def forloop[T](from: T)(check: (T) ⇒ Boolean)(next: (T) ⇒ T)(f: (T) ⇒ Unit): Unit
    Definition Classes
    CommonsDef
    Annotations
    @inline()
  10. def forloop(from: Int, until: Int, by: Int)(f: (Int) ⇒ Unit): Unit
    Definition Classes
    CommonsDef
    Annotations
    @inline()
  11. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  12. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. implicit def javaIterableToIterator[A](iterable: Iterable[A]): Iterator[A]
    Definition Classes
    CommonsDef
  15. implicit def javaIteratorAsScalaIterator[A](iterator: Iterator[A]): DualIterator[A]
    Definition Classes
    CommonsDef
  16. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. final def notify(): Unit
    Definition Classes
    AnyRef
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  19. def plotDescription(reader: SamSource, input: FilePath): String

    Gets a description for use in a generating a plot.

    Gets a description for use in a generating a plot. Returns the <sample> / <library> if there is only one sample and library, otherwise the input file name.

  20. implicit def scalaIteratorAsJavaIterator[A](iterator: Iterator[A]): DualIterator[A]
    Definition Classes
    CommonsDef
  21. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  22. def toString(): String
    Definition Classes
    AnyRef → Any
  23. def tryWith[A, B](resource: A, logger: Option[Logger])(cleanup: (A) ⇒ Unit)(doWork: (A) ⇒ B): Try[B]
    Definition Classes
    CommonsDef
  24. def tryWithCloseable[A <: Closeable](resource: A, logger: Option[Logger])(doWork: (A) ⇒ Unit): Try[Unit]
    Definition Classes
    CommonsDef
  25. def unreachable(message: ⇒ String): Nothing
    Definition Classes
    CommonsDef
  26. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  27. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. def yieldAndThen[A](it: ⇒ A)(block: ⇒ Unit): A
    Definition Classes
    CommonsDef

Inherited from CommonsDef

Inherited from AnyRef

Inherited from Any

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