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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  7. def equals(arg0: Any): Boolean
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  8. def errorProbabilityToPhred(p: Double): Int

    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

    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. val minValue: Int
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  18. def phredToErrorProbability(phred: Int): Double

    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.

  19. def phredToLogProbability(phred: Int): Double

    phred

    The phred score to convert.

    returns

    The input phred score as a log success probability.

  20. def phredToSuccessProbability(phred: Int): Double

    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.

  21. def successProbabilityToPhred(p: Double): Int

    p

    A success probability to convert to phred.

    returns

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

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