FlagstatCollector

Value Members

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

   

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2. final def ##(): Int

   

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3. def +=(other: FlagstatCollector): FlagstatCollector

   

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

   

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5. def addFunction(name: String, function: (SAMRecord) ⇒ Boolean): Unit

   

6. final def asInstanceOf[T0]: T0

   

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7. def clone(): AnyRef

   

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   protected[java.lang]

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8. var crossCounts: Array[Array[Long]]

   

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9. def crossReport(fraction: Boolean = false): String

   

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

    

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11. def equals(other: Any): Boolean

    

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    FlagstatCollector → AnyRef → Any

12. def finalize(): Unit

    

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    protected[java.lang]

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13. var functionCount: Int

    

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14. var functions: Array[(SAMRecord) ⇒ Boolean]

    

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

    

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16. def hashCode(): Int

    

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17. final def isInstanceOf[T0]: Boolean

    

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18. def loadDefaultFunctions(): Unit

    

19. def loadOrientationFunctions(): Unit

    

    This method will add functions to check orientation, for this a combination of flags and read positions are used.

20. def loadQualityFunctions(m: Int = 10, max: Int = 60): Unit

    

    The method will aditional checks based on mapping quality of the sam records.

    The method will aditional checks based on mapping quality of the sam records.

    m

    steps of quality

    max

    maximum quality

21. def loadRecord(record: SAMRecord): Unit

    

22. val names: Map[Int, String]

    

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

    

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24. final def notify(): Unit

    

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25. final def notifyAll(): Unit

    

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26. var readsCount: Int

    

27. def report: String

    

28. def summary: String

    

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

    

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30. def toString(): String

    

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31. def toSummaryMap: Map[String, Any]

    

32. var totalCounts: Array[Long]

    

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33. final def wait(): Unit

    

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

    

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

    

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36. def writeAsTsv(file: File): Unit

    

37. def writeReportToFile(outputFile: File): Unit

    

38. def writeSummaryTofile(outputFile: File): Unit