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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CommonsDef, Compat, AnyRef, Any
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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 ConstantAnnotation = ClassfileAnnotation
    Definition Classes
    Compat
  4. type DirPath = Path
    Definition Classes
    CommonsDef
  5. trait DualIterator[A] extends Iterator[A] with Iterator[A]
    Definition Classes
    CommonsDef
  6. 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 enumeratum.Enum#values method in your object, for example: def values: IndexedSeq[T] = findValues.

  7. type FilePath = Path
    Definition Classes
    CommonsDef
  8. type FilenamePrefix = String
    Definition Classes
    CommonsDef
  9. type FilenameSuffix = String
    Definition Classes
    CommonsDef
  10. case class GenomicRange(refName: String, start: Int, end: Int) extends Product with Serializable

    Stores information about the coordinates of the alternate locus

    Stores information about the coordinates of the alternate locus

    refName

    the name of the reference sequence (or chromosome)

    start

    position of the genomic range (1-based)

    end

    position of the gneomic range (1-based inclusive).

  11. implicit class IterableOnceMinByOption[A] extends AnyRef
  12. implicit class IteratorToJavaCollectionsAdapter[A] extends AnyRef
    Definition Classes
    CommonsDef
  13. implicit class MaxNBy[A] extends AnyRef
    Definition Classes
    CommonsDef
  14. class ParSupport[A, S <: Iterable[A], P <: ParIterable[A]] extends AnyRef
    Definition Classes
    CommonsDef
  15. type PathPrefix = Path
    Definition Classes
    CommonsDef
  16. type PathToBam = Path
    Definition Classes
    CommonsDef
  17. type PathToFasta = Path
    Definition Classes
    CommonsDef
  18. type PathToFastq = Path
    Definition Classes
    CommonsDef
  19. type PathToIntervals = Path
    Definition Classes
    CommonsDef
  20. type PathToSequenceDictionary = Path

    Represents a path to a sequence dictionary (.dict).

  21. type PathToVcf = Path
    Definition Classes
    CommonsDef
  22. implicit class SafelyClosable extends AnyRef
    Definition Classes
    CommonsDef
  23. implicit class SumBy[A] extends AnyRef
    Definition Classes
    CommonsDef
  24. type View[+A] = IterableView[A, Iterable[A]]
    Definition Classes
    Compat

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[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  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[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
    Annotations
    @native()
  12. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  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
    Annotations
    @native()
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  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 rangeToParSupport(r: Range): ParSupport[Int, Range, ParRange]
    Definition Classes
    CommonsDef
  21. implicit def scalaIteratorAsJavaIterator[A](iterator: Iterator[A]): DualIterator[A]
    Definition Classes
    CommonsDef
  22. implicit def seqToParSupport[A](seq: Seq[A]): ParSupport[A, _ <: Seq[A], _ <: ParSeq[A]]
    Definition Classes
    CommonsDef
  23. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  24. def toString(): String
    Definition Classes
    AnyRef → Any
  25. def tryWith[A, B](resource: A, logger: Option[Logger])(cleanup: (A) ⇒ Unit)(doWork: (A) ⇒ B): Try[B]
    Definition Classes
    CommonsDef
  26. def tryWithCloseable[A <: Closeable](resource: A, logger: Option[Logger])(doWork: (A) ⇒ Unit): Try[Unit]
    Definition Classes
    CommonsDef
  27. def unreachable(message: ⇒ String): Nothing
    Definition Classes
    CommonsDef
  28. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  31. def yieldAndThen[A](it: ⇒ A)(block: ⇒ Unit): A
    Definition Classes
    CommonsDef
  32. object GenomicRange extends Serializable

Deprecated Value Members

  1. def parseRange(range: String): GenomicRange

    Parses a genomic range of the form <chr>:<start>-<end> or <chr>:<start>, assuming the range is 1-based inclusive (closed-ended).

    Parses a genomic range of the form <chr>:<start>-<end> or <chr>:<start>, assuming the range is 1-based inclusive (closed-ended). If only a start position is included the range includes just the single base. Coordinates may include commas in the numbers.

    range

    the string to parse.

    Annotations
    @deprecated
    Deprecated

    (Since version 1.3.0) Use GenomicRange() instead

Inherited from CommonsDef

Inherited from Compat

Inherited from AnyRef

Inherited from Any

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