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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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.
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logProbabilityToPhred(p: Double): Int
- p
A log-scaled success probability to conver to phred.
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Returns this probability as a Phred score. If the log value is 0.0, we clip the phred score to Int.MaxValue.
- val minValue: Int
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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.
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def
phredToLogProbability(phred: Int): Double
- phred
The phred score to convert.
- returns
The input phred score as a log success probability.
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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.
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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.
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