Object

nl.biopet.tools.countalleles

CountAlleles

Related Doc: package countalleles

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object CountAlleles extends ToolCommand[Args]

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ToolCommand[Args], Logging, AnyRef, Any
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  1. CountAlleles
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Type Members

  1. case class AlleleCounts(count: Map[Allele, Int] = Map(), dp: Int = 0) extends Product with Serializable

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    Attributes
    protected

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
    CountAlleles → ToolCommand

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. def checkAlleles(samRecord: SAMRecord, vcfRecord: VariantContext): Option[String]

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  8. def clone(): AnyRef

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

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

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    Definition Classes
    ToolCommand

  10. def contactText: String

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    Definition Classes
    ToolCommand

  11. def contributingText: String

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    Definition Classes
    ToolCommand

  12. def countAlleles(vcfRecord: VariantContext, samReader: SamReader, readGroups: List[SAMReadGroupRecord]): Map[SAMReadGroupRecord, AlleleCounts]

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  13. def descriptionText: String

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    Definition Classes
    CountAlleles → ToolCommand

  14. def documentationText: String

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    Definition Classes
    ToolCommand

  15. def emptyArgs: Args

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    Definition Classes
    CountAlleles → ToolCommand

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

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    Definition Classes
    AnyRef

  17. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

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

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    Definition Classes
    ToolCommand

  19. def exampleText: String

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    Definition Classes
    CountAlleles → ToolCommand

  20. def finalize(): Unit

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

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

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    Definition Classes
    ToolCommand

  22. def generateReadme(outputFile: File): Unit

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    AnyRef → Any

  24. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  25. def installationText: String

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    Definition Classes
    ToolCommand

  26. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  27. def logger: Logger

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    Definition Classes
    Logging

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

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    Definition Classes
    CountAlleles → ToolCommand

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

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    Definition Classes
    ToolCommand

  30. def manualText: String

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    Definition Classes
    CountAlleles → ToolCommand

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

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    Definition Classes
    AnyRef

  32. final def notify(): Unit

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    Definition Classes
    AnyRef

  33. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    AnyRef

  38. def toString(): String

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    Definition Classes
    AnyRef → Any

  39. def toolName: String

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

  41. def urlToolName: String

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    Definition Classes
    ToolCommand

  42. def usageHeaders: List[String]

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    Attributes
    protected
    Definition Classes
    ToolCommand

  43. def usageHtmlTable: String

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    Definition Classes
    ToolCommand

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

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    Attributes
    protected
    Definition Classes
    ToolCommand

  45. def usageText: String

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    Definition Classes
    ToolCommand

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

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    Definition Classes
    ToolCommand

  47. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  49. 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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