VcfWithVcf

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

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

   

   Definition Classes

   AnyRef → Any

4. def aboutText: String

   

   Definition Classes

   ToolCommand

5. def argsParser: ArgsParser

   

   Definition Classes

   VcfWithVcf → ToolCommand

6. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

7. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   

   Definition Classes

   ToolCommand

9. def contactText: String

   

   Definition Classes

   ToolCommand

10. def contributingText: String

    

    Definition Classes

    ToolCommand

11. def createFieldMap(fields: List[Fields], record: VariantContext, secondaryRecords: List[VariantContext], header: VCFHeader): Map[String, List[Any]]

    

    Create Map of field -> List of attributes in secondary records

    Create Map of field -> List of attributes in secondary records

    fields

    List of Field

    record

    Original record

    secondaryRecords

    List of VariantContext with secondary records

    returns

    Map of fields and their values in secondary records

12. def createRecord(fieldMap: Map[String, List[Any]], record: VariantContext, fields: List[Fields], header: VCFHeader): VariantContext

    

13. def descriptionText: String

    

    Definition Classes

    VcfWithVcf → ToolCommand

14. def documentationText: String

    

    Definition Classes

    ToolCommand

15. def emptyArgs: Args

    

    Definition Classes

    VcfWithVcf → ToolCommand

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

    

    Definition Classes

    AnyRef

17. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

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

    

    Definition Classes

    ToolCommand

19. def exampleText: String

    

    Definition Classes

    VcfWithVcf → ToolCommand

20. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    

    Definition Classes

    ToolCommand

22. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef → Any

24. def getSecondaryField(record: VariantContext, secondaryRecord: VariantContext, field: String, header: VCFHeader): Any

    

    Get the proper representation of a field from a secondary record given an original record

    Get the proper representation of a field from a secondary record given an original record

    record

    original record

    secondaryRecord

    secondary record

    field

    field

    header

    header of secondary record

25. def getSecondaryRecords(secondaryReader: VCFFileReader, record: VariantContext, matchAllele: Boolean): List[VariantContext]

    

    Get secondary records matching the query record

    Get secondary records matching the query record

    secondaryReader

    reader for secondary records

    record

    query record

    matchAllele

    allele has to match query allele?

    returns

    List of VariantContext

26. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

27. def installationText: String

    

    Definition Classes

    ToolCommand

28. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

29. def logger: Logger

    

    Definition Classes

    Logging

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

    

    Definition Classes

    VcfWithVcf → ToolCommand

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

    

    Definition Classes

    ToolCommand

32. def manualText: String

    

    Definition Classes

    VcfWithVcf → ToolCommand

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

    

    Definition Classes

    AnyRef

34. final def notify(): Unit

    

    Definition Classes

    AnyRef

35. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

36. def numberA(referenceRecord: VariantContext, annotateRecord: VariantContext, field: String): List[Any]

    

    Get the correct values from a field that has number=A

    Get the correct values from a field that has number=A

    referenceRecord

    the reference record

    annotateRecord

    the to-be-annotated record

    field

    the field to annotate

37. def numberR(referenceRecord: VariantContext, annotateRecord: VariantContext, field: String): List[Any]

    

    Get the correct values from a field that has number=R

    Get the correct values from a field that has number=R

    referenceRecord

    the reference record

    annotateRecord

    the to-be-annotated record

    field

    the field to annotate

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef

42. def toString(): String

    

    Definition Classes

    AnyRef → Any

43. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

45. def urlToolName: String

    

    Definition Classes

    ToolCommand

46. def usageText: String

    

    Definition Classes

    ToolCommand

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( ... )