ADAM_2.12: Core 0.27.0 API < Back
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- ADAMShell
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o

org.bdgenomics.adam.util

# PhredUtils 

###

#### 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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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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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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17.  final def notifyAll(): Unit
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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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