Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

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3.  final def ==(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

4.  val BGEN_SUFFIX: String
5.  val INDEX_SUFFIX: String
6.  val NEXT_IDX_QUERY: String
7.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

8.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @native() @throws( ... )

9.  final def eq(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

10.  def equals(arg0: Any): Boolean

    Definition Classes

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11.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

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

12.  final def getClass(): Class[_]

    Definition Classes

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    @native()

13.  def getSampleIds(options: Map[String, String], hadoopConf: Configuration): Option[Seq[String]]

    Given a path to an Oxford-style .sample file exists (option: sampleFilePath), reads the sample IDs from the appropriate column (option: sampleIdColumn, default: ID_2).

    Given a path to an Oxford-style .sample file exists (option: sampleFilePath), reads the sample IDs from the appropriate column (option: sampleIdColumn, default: ID_2).

    If the column does not exist in the file, or if at least one row is malformed (does not contain a sample ID), an IllegalArgumentException is thrown. If no path is given, None is returned; if a valid path is given, Some list is returned.

14.  def hashCode(): Int

    Definition Classes

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    @native()

15.  def hlsJsonBuilder(options: Map[String, Any]): String

    Attributes

    protected

    Definition Classes

    HlsUsageLogging

16.  val idxLock: Striped[Lock]
17.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

18.  def logBgenRead(useIndex: Boolean): Unit
19.  lazy val logger: Logger

    Attributes

    protected

    Definition Classes

    LazyLogging

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

    Definition Classes

    AnyRef

21.  final def notify(): Unit

    Definition Classes

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    Annotations

    @native()

22.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

    Annotations

    @native()

23.  def recordHlsEvent(tag: String, options: Map[String, Any] = Map.empty): Unit

    Definition Classes

    HlsEventRecorder

24.  def recordHlsUsage(metric: MetricDefinition, tags: Map[TagDefinition, String] = Map.empty, blob: String = null): Unit

    Attributes

    protected

    Definition Classes

    HlsUsageLogging

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

    Definition Classes

    AnyRef

26.  def toString(): String

    Definition Classes

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27.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @native() @throws( ... )