GermlineCallerArgs

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. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7. var blockSize: Int

   Definition Classes

   ParquetArgs → ParquetRDDArgs

8. var chromosome: String

   Definition Classes

   ConcordanceArgs

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

10. var compressionCodec: CompressionCodecName

    Definition Classes

    ParquetArgs → ParquetRDDArgs

11. var disableDictionaryEncoding: Boolean

    Definition Classes

    ParquetArgs → ParquetRDDArgs

12. var doPrintUsage: Boolean

    Definition Classes

    Args4jBase

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

    Definition Classes

    AnyRef

14. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

15. var excludeIndels: Boolean

    Definition Classes

    ConcordanceArgs

16. var excludeSNVs: Boolean

    Definition Classes

    ConcordanceArgs

17. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

19. def hashCode(): Int

    Definition Classes

    AnyRef → Any

20. var includeDuplicates: Boolean

    Definition Classes

    ReadFilterArgs

21. var includeFailedQualityChecks: Boolean

    Definition Classes

    ReadFilterArgs

22. var includeSingleEnd: Boolean

    Definition Classes

    ReadFilterArgs

23. lazy val inputs: PerSample[Input]

    Definition Classes

    Base

24. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

25. var lociFile: String

    Attributes

    protected

    Definition Classes

    CallLociArgs

26. def lociFileOpt: Option[String]

    Definition Classes

    CallLociArgs

27. var lociStr: String

    Attributes

    protected

    Definition Classes

    CallLociArgs

28. def lociStrOpt: Option[String]

    Definition Classes

    CallLociArgs

29. var logLevel: String

    Definition Classes

    ParquetArgs

30. var maxGenotypes: Int

    Definition Classes

    GenotypeOutputArgs

31. var minAlignmentQuality: Int

    Definition Classes

    ReadFilterArgs

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

    Definition Classes

    AnyRef

33. var noSequenceDictionary: Boolean

    Definition Classes

    NoSequenceDictionaryArgs

34. final def notify(): Unit

    Definition Classes

    AnyRef

35. final def notifyAll(): Unit

    Definition Classes

    AnyRef

36. var onlyMappedReads: Boolean

    Definition Classes

    ReadFilterArgs

37. var outChunks: Int

    Definition Classes

    GenotypeOutputArgs

38. lazy val outputPathStr: String

    Definition Classes

    GenotypeOutputArgs

39. var pageSize: Int

    Definition Classes

    ParquetArgs → ParquetRDDArgs

40. def parseFilters(hadoopConfiguration: Configuration): InputFilters

    Definition Classes

    ReadFilterArgs

41. def paths: Array[String]

    Definition Classes

    SingleSampleArgs → Base

42. var printMetrics: Boolean

    Definition Classes

    Args4jBase

43. var reads: String

    Definition Classes

    SingleSampleArgs

44. def sampleName: String

    Definition Classes

    SingleSampleArgs

45. def sampleNames: Array[String]

    Definition Classes

    SingleSampleArgs → Base

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

    Definition Classes

    AnyRef

47. def toString(): String

    Definition Classes

    AnyRef → Any

48. var truthGenotypesFile: String

    Definition Classes

    ConcordanceArgs

49. def validate(sc: SparkContext): Unit

    Perform validation of command line arguments at startup.

    Perform validation of command line arguments at startup. This allows some late failures (e.g. output file already exists) to be surfaced more quickly.

    Definition Classes

    GenotypeOutputArgs

50. var variantOutput: String

    Definition Classes

    GenotypeOutputArgs

51. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

54. def writeVariants(genotypes: GenotypeRDD): Unit

    Write out an RDD of Genotype instances to a file.

    Write out an RDD of Genotype instances to a file.

    genotypes

    ADAM genotypes (i.e. the variants)

    Definition Classes

    GenotypeOutputArgs