VepNormalizer

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

   VepNormalizer → 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 createBuilder(record: VariantContext, removeCsq: Boolean): VariantContextBuilder

    

12. def csqCheck(header: VCFHeader): Unit

    

    Checks whether header has a CSQ tag

    Checks whether header has a CSQ tag

    header

    VCF header

13. def descriptionText: String

    

    Definition Classes

    VepNormalizer → ToolCommand

14. def documentationText: String

    

    Definition Classes

    ToolCommand

15. def emptyArgs: Args

    

    Definition Classes

    VepNormalizer → 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

    VepNormalizer → ToolCommand

20. def explodeTranscripts(record: VariantContext, csqInfos: Array[String], removeCsq: Boolean): Array[VariantContext]

    

    Explode a single VEP-annotated record to multiple normal records Based on the number of annotated transcripts in the CSQ tag

    Explode a single VEP-annotated record to multiple normal records Based on the number of annotated transcripts in the CSQ tag

    record

    the record as a VariantContext object

    csqInfos

    An array with names of new info tags

    returns

    An array with the new records

21. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    

    Definition Classes

    ToolCommand

23. def generateReadme(outputFile: File): Unit

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef → Any

25. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

26. def installationText: String

    

    Definition Classes

    ToolCommand

27. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

28. def logger: Logger

    

    Definition Classes

    Logging

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

    

    Definition Classes

    VepNormalizer → ToolCommand

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

    

    Definition Classes

    ToolCommand

31. def manualText: String

    

    Definition Classes

    VepNormalizer → ToolCommand

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

    

    Definition Classes

    AnyRef

33. def normalize(reader: VCFFileReader, writer: AsyncVariantContextWriter, newInfos: Array[String], mode: String, removeCsq: Boolean): Unit

    

    Normalizer

    Normalizer

    reader

    input VCF VCFFileReader

    writer

    output VCF AsyncVariantContextWriter

    newInfos

    array of string containing names of new info fields

    mode

    normalizer mode (explode or standard)

    removeCsq

    remove csq tag (Boolean)

34. final def notify(): Unit

    

    Definition Classes

    AnyRef

35. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

36. def parseCsq(record: VariantContext): Array[Array[String]]

    

37. def parseCsq(header: VCFHeader): Array[String]

    

    Parses the CSQ tag in the header

    Parses the CSQ tag in the header

    header

    the VCF header

    returns

    list of strings with new info fields

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. def standardTranscripts(record: VariantContext, csqInfos: Array[String], removeCsq: Boolean): VariantContext

    

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

    

    Definition Classes

    AnyRef

43. def toString(): String

    

    Definition Classes

    AnyRef → Any

44. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

46. def urlToolName: String

    

    Definition Classes

    ToolCommand

47. def usageText: String

    

    Definition Classes

    ToolCommand

48. def versionCheck(header: VCFHeader): Unit

    

    Checks whether version of input VCF is at least 4.0 VEP is known to cause issues below 4.0 Throws exception if not

    Checks whether version of input VCF is at least 4.0 VEP is known to cause issues below 4.0 Throws exception if not

    header

    VCFHeader of input VCF

49. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )