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org.bdgenomics.adam.util

PhredUtils

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object PhredUtils extends Serializable

Helper singleton for converting Phred scores to/from probabilities.

As a reminder, given an error probability \epsilon, the Phred score q is:

q = -10 log_{10} \epsilon

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

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  2. final def ##(): Int

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  7. def equals(arg0: Any): Boolean

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  8. def errorProbabilityToPhred(p: Double): Int

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    p

    An error probability to convert to phred.

    returns

    The input probability as a phred score, rounded to the nearest int.

  9. def finalize(): Unit

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  12. final def isInstanceOf[T0]: Boolean

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  13. def logProbabilityToPhred(p: Double): Int

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    p

    A log-scaled success probability to conver to phred.

    returns

    Returns this probability as a Phred score. If the log value is 0.0, we clip the phred score to Int.MaxValue.

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

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  15. final def notify(): Unit

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  16. final def notifyAll(): Unit

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  17. def phredToErrorProbability(phred: Int): Double

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    phred

    The phred score to convert.

    returns

    The input phred score as an error probability. If the phred score is above 255, we clip to 255.

  18. def phredToLogProbability(phred: Int): Double

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    phred

    The phred score to convert.

    returns

    The input phred score as a log success probability.

  19. def phredToSuccessProbability(phred: Int): Double

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    phred

    The phred score to convert.

    returns

    The input phred score as a success probability. If the phred score is above 255, we clip to 255.

  20. def successProbabilityToPhred(p: Double): Int

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    p

    A success probability to convert to phred.

    returns

    One minus the input probability as a phred score, rounded to the nearest int.

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

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  22. def toString(): String

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

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