Arguments

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 compressReadPartitions: Boolean

   Definition Classes

   PartitionedRegionsArgs

10. var doPrintUsage: Boolean

    Definition Classes

    Args4jBase

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

    Definition Classes

    AnyRef

12. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

13. var explodeCoverage: Boolean

    Definition Classes

    CappedRegionsPartitionerArgs

14. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

16. def halfWindowSize: Int

    Definition Classes

    HalfWindowConfig

17. def hashCode(): Int

    Definition Classes

    AnyRef → Any

18. var includeDuplicates: Boolean

    Definition Classes

    ReadFilterArgs

19. var includeFailedQualityChecks: Boolean

    Definition Classes

    ReadFilterArgs

20. var includeSingleEnd: Boolean

    Definition Classes

    ReadFilterArgs

21. lazy val inputs: PerSample[Input]

    Definition Classes

    Base

22. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

23. var lociFile: String

    Attributes

    protected

    Definition Classes

    CallLociArgs

24. def lociFileOpt: Option[String]

    Definition Classes

    CallLociArgs

25. var lociPartitionerName: String

    Attributes

    protected

    Definition Classes

    LociPartitionerArgs

26. 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

    PartitionedRegionsArgs → LociPartitionerArgs

27. var lociStr: String

    Attributes

    protected

    Definition Classes

    CallLociArgs

28. def lociStrOpt: Option[String]

    Definition Classes

    CallLociArgs

29. var maxReadsPerPartition: Int

    Definition Classes

    CappedRegionsPartitionerArgs

30. var minAlignmentQuality: Int

    Definition Classes

    ReadFilterArgs

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

    Definition Classes

    AnyRef

32. var noSequenceDictionary: Boolean

    Definition Classes

    NoSequenceDictionaryArgs

33. final def notify(): Unit

    Definition Classes

    AnyRef

34. final def notifyAll(): Unit

    Definition Classes

    AnyRef

35. def numPartitions(sc: SparkContext): Int

    Definition Classes

    UniformPartitionerArgs

36. var onlyMappedReads: Boolean

    Definition Classes

    ReadFilterArgs

37. var output: String

38. var parallelism: NumPartitions

    Attributes

    protected

    Definition Classes

    UniformPartitionerArgs

39. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes

    ReadFilterArgs

40. def partitionedReadsPathOpt: Option[String]

    Definition Classes

    PartitionedRegionsArgs

41. 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

42. var paths: Array[String]

    Definition Classes

    Arguments → Base

43. var printMetrics: Boolean

    Definition Classes

    Args4jBase

44. var printPartitioningStats: Boolean

    Definition Classes

    LociPartitionerArgs

45. def reference(sc: SparkContext): ReferenceBroadcast

    Definition Classes

    HasReference

46. var referenceIsPartial: Boolean

    Definition Classes

    ReferenceArgs → HasReference

47. var referencePath: String

    Definition Classes

    ReferenceArgs → HasReference

48. var sampleNames: Array[String]

    Definition Classes

    Arguments → Base

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

    Definition Classes

    AnyRef

50. def toString(): String

    Definition Classes

    AnyRef → Any

51. var trimRanges: Boolean

    Definition Classes

    CappedRegionsPartitionerArgs

52. def validate(sc: SparkContext): Unit

    Definition Classes

    Args

53. var variants: String

54. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )