Package htsjdk.samtools.util
Class QualityUtil
- java.lang.Object
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- htsjdk.samtools.util.QualityUtil
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public final class QualityUtil extends Object
Utility class for working with quality scores and error probabilities.
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Constructor Summary
Constructors Constructor Description QualityUtil()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static double
getErrorProbabilityFromPhredScore(int i)
Given a phred score between 0 and 100 returns the probability of error.static int
getPhredScoreFromErrorProbability(double probability)
Gets the phred score for any given probability of error.static int
getPhredScoreFromObsAndErrors(double observations, double errors)
Gets the phred score given the specified observations and errors.static double
sumOfErrorProbabilities(SAMRecord rec)
Calculates the sum of error probabilities for all read bases in the SAM record.
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Method Detail
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getErrorProbabilityFromPhredScore
public static double getErrorProbabilityFromPhredScore(int i)
Given a phred score between 0 and 100 returns the probability of error.
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getPhredScoreFromErrorProbability
public static int getPhredScoreFromErrorProbability(double probability)
Gets the phred score for any given probability of error.
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getPhredScoreFromObsAndErrors
public static int getPhredScoreFromObsAndErrors(double observations, double errors)
Gets the phred score given the specified observations and errors.
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sumOfErrorProbabilities
public static double sumOfErrorProbabilities(SAMRecord rec)
Calculates the sum of error probabilities for all read bases in the SAM record. Takes the SAM record as opposed to the qualities directly so that it can make sure to count no-calls as 1 instead of what the quality score says.
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