VcfStatsSpark

Value Members

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

   

   Definition Classes

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2. final def ##(): Int

   

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

   

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4. def aboutText: String

   

   Definition Classes

   ToolCommand

5. def argsParser: ArgsParser

   

   Definition Classes

   VcfStatsSpark → ToolCommand

6. final def asInstanceOf[T0]: T0

   

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   Any

7. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

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   @throws( ... )

8. def cmdArrayToArgs(args: Array[String]): Args

   

   Definition Classes

   ToolCommand

9. def contactText: String

   

   Definition Classes

   ToolCommand

10. def contigDir(outputDir: File, contig: String): File

    

    Returns the contig dir of a given contig

11. def contigGeneralStats(vcfRecords: RDD[VariantContext], cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String): (Option[FutureAction[Unit]], Option[RDD[(String, GeneralStats)]])

    

    This will generate contigs stats and write this if this is not disabled

12. def contigGenotypeFieldCounts(vcfRecords: RDD[VariantContext], header: Broadcast[VCFHeader], cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String): Map[VcfField, (Option[Future[Unit]], RDD[(String, GenotypeFieldCounts)])]

    

    This will generate contigs stats and write this if this is not disabled

13. def contigGenotypeStats(vcfRecords: RDD[VariantContext], header: Broadcast[VCFHeader], cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String): (Option[FutureAction[Unit]], Option[RDD[(String, GenotypeStats)]])

    

    This will generate contigs stats and write this if this is not disabled

14. def contigInfoFieldCounts(vcfRecords: RDD[VariantContext], header: Broadcast[VCFHeader], cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String): Map[VcfField, (Option[Future[Unit]], RDD[(String, InfoFieldCounts)])]

    

    This will generate contigs stats and write this if this is not disabled

15. def contigSampleCompare(vcfRecords: RDD[VariantContext], header: Broadcast[VCFHeader], cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String): (Option[FutureAction[Unit]], Option[RDD[(String, SampleCompare)]])

    

    This will generate contigs stats and write this if this is not disabled

16. def contigSampleDistributions(vcfRecords: RDD[VariantContext], cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String): (Option[FutureAction[Unit]], Option[RDD[(String, SampleDistributions)]])

    

    This will generate contigs stats and write this if this is not disabled

17. def contributingText: String

    

    Definition Classes

    ToolCommand

18. def descriptionText: String

    

    Definition Classes

    VcfStatsSpark → ToolCommand

19. def documentationText: String

    

    Definition Classes

    ToolCommand

20. def emptyArgs: Args

    

    Definition Classes

    VcfStatsSpark → ToolCommand

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

    

    Definition Classes

    AnyRef

22. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

23. def example(args: String*): String

    

    Definition Classes

    ToolCommand

24. def exampleText: String

    

    Definition Classes

    VcfStatsSpark → ToolCommand

25. def finalize(): Unit

    

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    protected[java.lang]

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

26. def generateDocumentation(outputDirectory: File, version: String, release: Boolean): Unit

    

    Definition Classes

    ToolCommand

27. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

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29. def hashCode(): Int

    

    Definition Classes

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30. def installationText: String

    

    Definition Classes

    ToolCommand

31. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

32. def loadVcfFile(cmdArgs: Broadcast[Args], regions: Broadcast[List[BedRecord]], prefixMessage: String, sorting: Boolean = true, countJob: Boolean = true, cache: Boolean = true)(implicit sc: SparkContext): RDD[VariantContext]

    

    This method will load a list of regions into memory

33. def logger: Logger

    

    Definition Classes

    Logging

34. def main(args: Array[String]): Unit

    

    Main entry point from the commandline

    Main entry point from the commandline

    Definition Classes

    VcfStatsSpark → ToolCommand

35. def mainFromArgs(cmdArgs: Args): Unit

    

    API entry point

36. def mainPageContents: List[(String, String)]

    

    Definition Classes

    ToolCommand

37. def manualText: String

    

    Definition Classes

    VcfStatsSpark → ToolCommand

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

    

    Definition Classes

    AnyRef

39. final def notify(): Unit

    

    Definition Classes

    AnyRef

40. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

41. def processContig(regions: Broadcast[List[BedRecord]], cmdArgs: Broadcast[Args], header: Broadcast[VCFHeader], contig: Option[String])(implicit sc: SparkContext): ChunkResult

    

    This method will execute a list of regions.

42. def processContigTotal(regions: Broadcast[List[BedRecord]], cmdArgs: Broadcast[Args], header: Broadcast[VCFHeader], contig: Option[String])(implicit sc: SparkContext): (Future[Unit], RDD[(String, StatsTotal)])

    

43. def readmeContents: List[(String, String)]

    

    Definition Classes

    ToolCommand

44. def sparkExample(args: String*): String

    

    Definition Classes

    ToolCommand

45. def sparkUnsafeExample(args: String*): String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

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47. def toString(): String

    

    Definition Classes

    AnyRef → Any

48. def toolName: String

    

    Definition Classes

    ToolCommand

49. def totalContigGenotypeFieldCounts(contigs: Map[VcfField, List[RDD[(String, GenotypeFieldCounts)]]], header: Broadcast[VCFHeader], cmdArgs: Broadcast[Args])(implicit sc: SparkContext): Option[Future[Any]]

    

    This will combine contigs stats and write the output file

50. def totalContigInfoFieldCounts(contigs: Map[VcfField, List[RDD[(String, InfoFieldCounts)]]], header: Broadcast[VCFHeader], cmdArgs: Broadcast[Args])(implicit sc: SparkContext): Option[Future[Any]]

    

    This will combine contigs stats and write the output file

51. def totalGeneralStats(generalContig: List[RDD[(String, GeneralStats)]], cmdArgs: Broadcast[Args])(implicit sc: SparkContext): Option[Future[Unit]]

    

    This will combine contigs stats and write the output file

52. def totalGenotypeStats(contigs: List[RDD[(String, GenotypeStats)]], cmdArgs: Broadcast[Args], header: Broadcast[VCFHeader])(implicit sc: SparkContext): Option[Future[Unit]]

    

    This will combine contigs stats and write the output file

53. def totalSampleCompare(contigs: List[RDD[(String, SampleCompare)]], cmdArgs: Broadcast[Args], header: Broadcast[VCFHeader])(implicit sc: SparkContext): Option[Future[Unit]]

    

    This will combine contigs stats and write the output file

54. def totalSampleDistributions(contigs: List[RDD[(String, SampleDistributions)]], cmdArgs: Broadcast[Args])(implicit sc: SparkContext): Option[Future[Unit]]

    

    This will combine contigs stats and write the output file

55. def unsafeExample(args: String*): String

    

    Definition Classes

    ToolCommand

56. def urlToolName: String

    

    Definition Classes

    ToolCommand

57. def usageHeaders: List[String]

    

    Attributes

    protected

    Definition Classes

    ToolCommand

58. def usageHtmlTable: String

    

    Definition Classes

    ToolCommand

59. def usageRows(parser: OptionParser[Args]): List[List[String]]

    

    Attributes

    protected

    Definition Classes

    ToolCommand

60. def usageText: String

    

    Definition Classes

    ToolCommand

61. def validateArgs(args: String*): Unit

    

    Definition Classes

    ToolCommand

62. final def wait(): Unit

    

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

    

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

    

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    @throws( ... )