ValidateFastq

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. val allowedBases: Regex

   

6. def argsParser: ArgsParser

   

   Definition Classes

   ValidateFastq → ToolCommand

7. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

8. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

   

   Definition Classes

   ToolCommand

10. def contactText: String

    

    Definition Classes

    ToolCommand

11. def contributingText: String

    

    Definition Classes

    ToolCommand

12. def descriptionText: String

    

    Definition Classes

    ValidateFastq → ToolCommand

13. def documentationText: String

    

    Definition Classes

    ToolCommand

14. def duplicateCheck(current: FastqRecord, before: Option[FastqRecord]): Unit

    

    This function checks for duplicates.

    This function checks for duplicates.

    current

    currect fastq record

    before

    fastq record before the current record

    Exceptions thrown

    IllegalStateException Throws this when an error is ofund during checking

15. def emptyArgs: Args

    

    Definition Classes

    ValidateFastq → 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

    ValidateFastq → 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 hashCode(): Int

    

    Definition Classes

    AnyRef → Any

25. def installationText: String

    

    Definition Classes

    ToolCommand

26. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

27. def logger: Logger

    

    Definition Classes

    Logging

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

    

    Definition Classes

    ValidateFastq → ToolCommand

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

    

    Definition Classes

    ToolCommand

30. def manualText: String

    

    Definition Classes

    ValidateFastq → ToolCommand

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

    

    Definition Classes

    AnyRef

32. final def notify(): Unit

    

    Definition Classes

    AnyRef

33. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef

38. def toString(): String

    

    Definition Classes

    AnyRef → Any

39. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

41. def urlToolName: String

    

    Definition Classes

    ToolCommand

42. def usageHeaders: List[String]

    

    Attributes

    protected

    Definition Classes

    ToolCommand

43. def usageHtmlTable: String

    

    Definition Classes

    ToolCommand

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

    

    Attributes

    protected

    Definition Classes

    ToolCommand

45. def usageText: String

    

    Definition Classes

    ToolCommand

46. def validFastqRecord(record: FastqRecord): Unit

    

    This method will check if fastq record is correct

    This method will check if fastq record is correct

    record

    Fastq record to check

    Exceptions thrown

    IllegalStateException Throws this when an error is ofund during checking

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

    

    Definition Classes

    ToolCommand

48. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )