ExtractAdaptersFastqc

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

   ExtractAdaptersFastqc → ToolCommand

6. final def asInstanceOf[T0]: T0

   

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   Any

7. def clone(): AnyRef

   

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   protected[java.lang]

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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 descriptionText: String

    

    Definition Classes

    ExtractAdaptersFastqc → ToolCommand

12. def documentationText: String

    

    Definition Classes

    ToolCommand

13. def emptyArgs: Args

    

    Definition Classes

    ExtractAdaptersFastqc → ToolCommand

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

    

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15. def equals(arg0: Any): Boolean

    

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

    

    Definition Classes

    ToolCommand

17. def exampleText: String

    

    Definition Classes

    ExtractAdaptersFastqc → ToolCommand

18. def finalize(): Unit

    

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    protected[java.lang]

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19. def foundAdapters(fastqcModules: Map[String, FastQCModule], adapterCutoff: Double, adapterSet: Set[AdapterSequence]): Set[AdapterSequence]

    

    This method will find the adapters sequences from the fastqc data

    This method will find the adapters sequences from the fastqc data

    fastqcModules

    Content of the fastqc data file

    adapterCutoff

    Cutoff for adapters

    adapterSet

    Known sequences

    returns

    Found sequences

20. def foundOverrepresented(fastqcModules: Map[String, FastQCModule], contaminantSet: Set[AdapterSequence]): Set[AdapterSequence]

    

    This method will find the overrepresented sequences from the fastqc data

    This method will find the overrepresented sequences from the fastqc data

    fastqcModules

    Content of the fastqc data file

    contaminantSet

    Known sequences

    returns

    Found sequences

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

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24. def getFastqcSeqs(file: File): Set[AdapterSequence]

    

    This will read known sequences

25. def hashCode(): Int

    

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26. def installationText: String

    

    Definition Classes

    ToolCommand

27. final def isInstanceOf[T0]: Boolean

    

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28. def logger: Logger

    

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    Logging

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

    

    Definition Classes

    ExtractAdaptersFastqc → ToolCommand

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

    

    Definition Classes

    ToolCommand

31. def manualText: String

    

    Definition Classes

    ExtractAdaptersFastqc → ToolCommand

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

    

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33. final def notify(): Unit

    

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34. final def notifyAll(): Unit

    

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35. def qcModules(dataFile: File): Map[String, FastQCModule]

    

    FastQC QC modules.

    FastQC QC modules.

    dataFile

    File to read

    returns

    Mapping of FastQC module names and its contents as array of strings (one item per line)

    Exceptions thrown

    FileNotFoundException if the FastQC data file can not be found.

    IllegalStateException if the module lines have no content or mapping is empty.

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

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

    

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40. def toString(): String

    

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41. def toolName: String

    

    Definition Classes

    ToolCommand

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

    

    Definition Classes

    ToolCommand

43. def urlToolName: String

    

    Definition Classes

    ToolCommand

44. def usageHeaders: List[String]

    

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    protected

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    ToolCommand

45. def usageHtmlTable: String

    

    Definition Classes

    ToolCommand

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

    

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    protected

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    ToolCommand

47. def usageText: String

    

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    ToolCommand

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

    

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    ToolCommand

49. final def wait(): Unit

    

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

    

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

    

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52. def writeOutput(sequences: Set[AdapterSequence], outputFile: Option[File], outputAsFasta: Boolean = false): Unit

    

    This will write the output to a file or to stdout when none file supplied