QualityUtil (htsjdk 4.1.2 API)

java.lang.Object

htsjdk.samtools.util.QualityUtil

public final class QualityUtil extends Object

Utility class for working with quality scores and error probabilities.

Constructor Summary

Constructors

Constructor

Description

QualityUtil()
Method Summary

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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- QualityUtil
  
  public QualityUtil()
Method Details
- getErrorProbabilityFromPhredScore
  
  public static double getErrorProbabilityFromPhredScore(int i)
  
  Given a phred score between 0 and 100 returns the probability of error.
- getPhredScoreFromErrorProbability
  
  public static int getPhredScoreFromErrorProbability(double probability)
  
  Gets the phred score for any given probability of error.
- getPhredScoreFromObsAndErrors
  
  public static int getPhredScoreFromObsAndErrors(double observations, double errors)
  
  Gets the phred score given the specified observations and errors.
- 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.