org.bdgenomics.adam.rdd.read.recalibration

BaseQualityRecalibration

class BaseQualityRecalibration extends Serializable with Logging

The algorithm proceeds in two phases. First, we make a pass over the reads to collect statistics and build the recalibration tables. Then, we perform a second pass over the reads to apply the recalibration and assign adjusted quality scores.

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Instance Constructors

  1. new BaseQualityRecalibration(input: RDD[(Option[DecadentRead], Option[AlignmentRecord])], knownSnps: Broadcast[SnpTable], dumpObservationTableFile: Option[String] = scala.None)

Value Members

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

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

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  3. final def ##(): Int

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

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

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  6. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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    @throws( ... )
  8. val covariates: CovariateSpace

  9. val dataset: RDD[(CovariateKey, Residue)]

  10. val dumpObservationTableFile: Option[String]

  11. val enableVisitLogging: Boolean

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

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  13. def equals(arg0: Any): Boolean

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  14. def finalize(): Unit

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    @throws( classOf[java.lang.Throwable] )
  15. final def getClass(): Class[_]

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  16. def hashCode(): Int

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  17. val input: RDD[(Option[DecadentRead], Option[AlignmentRecord])]

  18. final def isInstanceOf[T0]: Boolean

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  19. def isTraceEnabled(): Boolean

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  20. val knownSnps: Broadcast[SnpTable]

  21. def log: Logger

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  22. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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  23. def logDebug(msg: ⇒ String): Unit

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  24. def logError(msg: ⇒ String, throwable: Throwable): Unit

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  25. def logError(msg: ⇒ String): Unit

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  26. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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  27. def logInfo(msg: ⇒ String): Unit

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  28. def logName: String

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  29. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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  30. def logTrace(msg: ⇒ String): Unit

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  31. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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  32. def logWarning(msg: ⇒ String): Unit

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  33. val minAcceptableQuality: QualityScore

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

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  35. final def notify(): Unit

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  36. final def notifyAll(): Unit

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  37. val observed: ObservationTable

  38. val result: RDD[AlignmentRecord]

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

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  40. def toString(): String

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  41. final def wait(): Unit

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

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

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