PartitionLociArgs

Value Members

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

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

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

   Definition Classes

   Any

6. var _lociPartitioningPathOpt: Option[String]

   Attributes

   protected

   Definition Classes

   LociPartitionerArgs

7. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

8. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

9. var doPrintUsage: Boolean

   Definition Classes

   Args4jBase

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

    Definition Classes

    AnyRef

11. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

12. var explodeCoverage: Boolean

    Definition Classes

    CappedRegionsPartitionerArgs

13. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

15. def halfWindowSize: Int

    Definition Classes

    HalfWindowArgs → HalfWindowConfig

16. def hashCode(): Int

    Definition Classes

    AnyRef → Any

17. var includeDuplicates: Boolean

    Definition Classes

    ReadFilterArgs

18. var includeFailedQualityChecks: Boolean

    Definition Classes

    ReadFilterArgs

19. var includeSingleEnd: Boolean

    Definition Classes

    ReadFilterArgs

20. lazy val inputs: PerSample[Input]

    Definition Classes

    Base

21. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

22. var lociFile: String

    Attributes

    protected

    Definition Classes

    CallLociArgs

23. def lociFileOpt: Option[String]

    Definition Classes

    CallLociArgs

24. var lociPartitionerName: String

    Attributes

    protected

    Definition Classes

    LociPartitionerArgs

25. def lociPartitioningPathOpt: Option[String]

    Simple getter interface here supports overriding behavior here to support different resolution logic, cf.

    Simple getter interface here supports overriding behavior here to support different resolution logic, cf. PartitionedRegionsArgs.

    Definition Classes

    LociPartitionerArgs

26. var lociStr: String

    Attributes

    protected

    Definition Classes

    CallLociArgs

27. def lociStrOpt: Option[String]

    Definition Classes

    CallLociArgs

28. var maxReadsPerPartition: Int

    Definition Classes

    CappedRegionsPartitionerArgs

29. var minAlignmentQuality: Int

    Definition Classes

    ReadFilterArgs

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

    Definition Classes

    AnyRef

31. var noSequenceDictionary: Boolean

    Definition Classes

    NoSequenceDictionaryArgs

32. final def notify(): Unit

    Definition Classes

    AnyRef

33. final def notifyAll(): Unit

    Definition Classes

    AnyRef

34. def numPartitions(sc: SparkContext): Int

    Definition Classes

    UniformPartitionerArgs

35. var onlyMappedReads: Boolean

    Definition Classes

    ReadFilterArgs

36. var parallelism: NumPartitions

    Attributes

    protected

    Definition Classes

    UniformPartitionerArgs

37. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes

    ReadFilterArgs

38. var partitioningAccuracy: NumMicroPartitions

    Long >= 1.

    Long >= 1. Number of micro-partitions generated for each of the numPartitions Spark partitions that will be computed. Higher values of this will result in a more exact but more expensive computation. In the extreme, setting this to greater than the number of loci (per partition) will result in an exact calculation.

    Definition Classes

    MicroRegionPartitionerArgs

39. var paths: Array[String]

    Definition Classes

    Arguments → Base

40. var printMetrics: Boolean

    Definition Classes

    Args4jBase

41. var printPartitioningStats: Boolean

    Definition Classes

    LociPartitionerArgs

42. var sampleNames: Array[String]

    Definition Classes

    Arguments → Base

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

    Definition Classes

    AnyRef

44. def toString(): String

    Definition Classes

    AnyRef → Any

45. var trimRanges: Boolean

    Definition Classes

    CappedRegionsPartitionerArgs

46. def validate(sc: SparkContext): Unit

    Definition Classes

    Args

47. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )