Object

nl.biopet.tools.sampleconfig.casecontrol

CaseControl

Related Doc: package casecontrol

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object CaseControl extends ToolCommand[Args]

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ToolCommand[Args], Logging, AnyRef, Any
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Inherited
  1. CaseControl
  2. ToolCommand
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Type Members

  1. case class CaseControl(inputName: String, inputFile: IndexedBamFile, controlName: String, controlFile: IndexedBamFile) extends Product with Serializable

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  2. case class CaseControls(caseControls: List[CaseControl]) extends Product with Serializable

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  3. case class IndexedBamFile(file: String, index: String) extends Product with Serializable

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    AnyRef → Any

  4. def aboutText: String

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    Definition Classes
    ToolCommand

  5. def argsParser: ArgsParser

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    Definition Classes
    CaseControl → ToolCommand

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. implicit val caseControlReads: Reads[CaseControl]

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  8. implicit val caseControlWrites: Writes[CaseControl]

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  9. implicit val caseControlsReads: Reads[CaseControls]

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  10. implicit val caseControlsWrites: Writes[CaseControls]

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  11. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    ToolCommand

  13. def contactText: String

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    Definition Classes
    ToolCommand

  14. def contributingText: String

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    Definition Classes
    ToolCommand

  15. def createFileMap(files: List[File]): Map[String, IndexedBamFile]

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    This will create a map of bamfiles including the index files

    This will create a map of bamfiles including the index files

    files

    bam files

  16. def createPairs(config: SampleConfig, fileMap: Map[String, IndexedBamFile], controlTag: String = "control"): CaseControls

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    This will create the control pairs

    This will create the control pairs

    config

    SampleConfig

    fileMap

    bam files

    controlTag

    control tag, default "control"

  17. def descriptionText: String

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    Definition Classes
    CaseControl → ToolCommand

  18. def documentationText: String

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    Definition Classes
    ToolCommand

  19. def emptyArgs: Args

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    Definition Classes
    CaseControl → ToolCommand

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

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    Definition Classes
    AnyRef

  21. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    ToolCommand

  23. def exampleText: String

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    Definition Classes
    CaseControl → ToolCommand

  24. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

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    Definition Classes
    ToolCommand

  26. def generateReadme(outputFile: File): Unit

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    AnyRef → Any

  28. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  29. implicit val indexedBamFileReads: Reads[IndexedBamFile]

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  30. implicit val indexedBamFileWrites: Writes[IndexedBamFile]

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  31. def installationText: String

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    Definition Classes
    ToolCommand

  32. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  33. def logger: Logger

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    Definition Classes
    Logging

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

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    Definition Classes
    CaseControl → ToolCommand

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

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    Definition Classes
    ToolCommand

  36. def manualText: String

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    Definition Classes
    CaseControl → ToolCommand

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

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    Definition Classes
    AnyRef

  38. final def notify(): Unit

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    Definition Classes
    AnyRef

  39. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    AnyRef

  44. def toString(): String

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    Definition Classes
    AnyRef → Any

  45. def toolName: String

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

  47. def urlToolName: String

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    Definition Classes
    ToolCommand

  48. def usageHeaders: List[String]

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    Attributes
    protected
    Definition Classes
    ToolCommand

  49. def usageHtmlTable: String

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    Definition Classes
    ToolCommand

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

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    Attributes
    protected
    Definition Classes
    ToolCommand

  51. def usageText: String

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

  53. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ToolCommand[Args]

Inherited from Logging

Inherited from AnyRef

Inherited from Any

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