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 checkMate(r1: FastqRecord, r2: FastqRecord): Unit

   

   This method checks if the pair is the same ID

   This method checks if the pair is the same ID

   r1

   R1 fastq record

   r2

   R2 fastq record

   Exceptions thrown

   IllegalStateException Throws this when an error is ofund during checking

9. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

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

    

    Definition Classes

    ToolCommand

11. def contactText: String

    

    Definition Classes

    ToolCommand

12. def contributingText: String

    

    Definition Classes

    ToolCommand

13. def descriptionText: String

    

    Definition Classes

    ValidateFastq → ToolCommand

14. def documentationText: String

    

    Definition Classes

    ToolCommand

15. 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

16. def emptyArgs: Args

    

    Definition Classes

    ValidateFastq → ToolCommand

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

    

    Definition Classes

    AnyRef

18. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

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

    

    Definition Classes

    ToolCommand

20. def exampleText: String

    

    Definition Classes

    ValidateFastq → ToolCommand

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

    ValidateFastq → ToolCommand

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

    

    Definition Classes

    ToolCommand

31. def manualText: String

    

    Definition Classes

    ValidateFastq → ToolCommand

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

    

    Definition Classes

    AnyRef

33. final def notify(): Unit

    

    Definition Classes

    AnyRef

34. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    AnyRef

39. def toString(): String

    

    Definition Classes

    AnyRef → Any

40. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

42. def urlToolName: String

    

    Definition Classes

    ToolCommand

43. def usageText: String

    

    Definition Classes

    ToolCommand

44. 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

45. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )