org.bdgenomics.adam.rdd.recalibration

BaseQualityRecalibration

class BaseQualityRecalibration extends Serializable with Logging

Base Quality Score Recalibration

The algorithm proceeds in two phases:

  1. Make a pass over the reads to collect statistics and build the recalibration tables.

2. 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[DecadentRead], knownSnps: Broadcast[SnpTable])

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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  7. def clone(): AnyRef

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    @throws( ... )

  8. val covariates: CovariateSpace

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

  10. val dumpObservationTable: Boolean

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

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  16. def hashCode(): Int

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  17. val input: RDD[DecadentRead]

  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 logTrace(msg: ⇒ String, throwable: Throwable): Unit

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

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

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

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  32. val minAcceptableQuality: QualityScore

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

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  34. final def notify(): Unit

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  35. final def notifyAll(): Unit

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  36. val observed: ObservationTable

  37. val result: RDD[ADAMRecord]

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

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  39. def toString(): String

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  40. final def wait(): Unit

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

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

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