BgenFileFormat

Value Members

1. final def !=(arg0: Any): Boolean

   

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2. final def ##(): Int

   

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3. final def ==(arg0: Any): Boolean

   

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4. val BGEN_SUFFIX: String

   

5. val INDEX_SUFFIX: String

   

6. val NEXT_IDX_QUERY: String

   

7. final def asInstanceOf[T0]: T0

   

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   Any

8. def clone(): AnyRef

   

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   protected[java.lang]

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

   

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10. def equals(arg0: Any): Boolean

    

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11. def finalize(): Unit

    

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    protected[java.lang]

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

12. final def getClass(): Class[_]

    

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

    

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    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

    

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    protected

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    LazyLogging → Logging

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

    

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21. final def notify(): Unit

    

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22. final def notifyAll(): Unit

    

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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

    

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26. def toString(): String

    

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27. final def wait(): Unit

    

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    @throws( ... )

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

    

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

    

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