Package Accuracy

Class AccuracyStats


  • public class AccuracyStats
    extends java.lang.Object
    Represents accuracy statistics
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double accuracy()
      Returns the overall accuracy
      int correct()
      Return the total number of genotypes that are correct
      double correlation()
      Returns the overall correlation
      double depthAccuracy​(int depth)
      Returns the accuracy for a certain depth (number of reads)
      int depthCorrect​(int depth)
      Return the number of genotypes that are correct that have the given depth (read count)
      double depthCorrelation​(int depth)
      Returns the correlation for a certain depth (number of reads)
      double depthGenoAccuracy​(int depth, byte geno)
      Return the accuracy for a given depth (read count) and true genotype
      int depthGenoCorrect​(int depth, byte geno)
      Return the number of genotypes that are correct that have the given depth (read count) and true genotype
      int depthGenoTotal​(int depth, byte geno)
      Return the number of genotypes used in the accuracy calculation that have the give depth (read count) and true genotype
      int depthTotal​(int depth)
      Return the number of genotypes used in the accuracy calculation that have the given depth (read count)
      double genoAccuracy​(byte geno)
      Return the accuracy for a given genotype
      int genoCorrect​(byte geno)
      Return the number of genotypes that are correct that have the give true genotype
      int genoTotal​(byte geno)
      Return the number of genotypes used in the accuracy calculation that have the give true genotype
      int getMaxDepth()
      Gte the maximum depth (read count) of any genotype used in the accuracy calculation
      int total()
      Return the total number of genotypes used in the accuracy calculation
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • accuracy

        public double accuracy()
        Returns the overall accuracy
        Returns:
        The overall accuracy
      • correlation

        public double correlation()
        Returns the overall correlation
        Returns:
        The overall correlation
      • depthAccuracy

        public double depthAccuracy​(int depth)
        Returns the accuracy for a certain depth (number of reads)
        Parameters:
        depth - The depth to return the accuracy for
        Returns:
        The accuracy
      • depthCorrelation

        public double depthCorrelation​(int depth)
        Returns the correlation for a certain depth (number of reads)
        Parameters:
        depth - The depth to return the accuracy for
        Returns:
        The correlation
      • genoAccuracy

        public double genoAccuracy​(byte geno)
        Return the accuracy for a given genotype
        Parameters:
        geno - The true genotype to return the accuracy for
        Returns:
        The accuracy
      • depthGenoAccuracy

        public double depthGenoAccuracy​(int depth,
                                        byte geno)
        Return the accuracy for a given depth (read count) and true genotype
        Parameters:
        depth - The depth to return the accuracy for
        geno - The true genotype to return the accuracy for
        Returns:
        The accuracy
      • total

        public int total()
        Return the total number of genotypes used in the accuracy calculation
        Returns:
        The number of genotypes
      • depthTotal

        public int depthTotal​(int depth)
        Return the number of genotypes used in the accuracy calculation that have the given depth (read count)
        Parameters:
        depth - Depth
        Returns:
        The number of genotypes
      • genoTotal

        public int genoTotal​(byte geno)
        Return the number of genotypes used in the accuracy calculation that have the give true genotype
        Parameters:
        geno - The true genotype
        Returns:
        The number of genotypes
      • depthGenoTotal

        public int depthGenoTotal​(int depth,
                                  byte geno)
        Return the number of genotypes used in the accuracy calculation that have the give depth (read count) and true genotype
        Parameters:
        depth - Depth
        geno - The true genotype
        Returns:
        The number of genotypes
      • correct

        public int correct()
        Return the total number of genotypes that are correct
        Returns:
        The number of genotypes
      • depthCorrect

        public int depthCorrect​(int depth)
        Return the number of genotypes that are correct that have the given depth (read count)
        Parameters:
        depth - Depth
        Returns:
        The number of genotypes
      • genoCorrect

        public int genoCorrect​(byte geno)
        Return the number of genotypes that are correct that have the give true genotype
        Parameters:
        geno - The true genotype
        Returns:
        The number of genotypes
      • depthGenoCorrect

        public int depthGenoCorrect​(int depth,
                                    byte geno)
        Return the number of genotypes that are correct that have the given depth (read count) and true genotype
        Parameters:
        depth - Depth
        geno - The true genotype
        Returns:
        The number of genotypes
      • getMaxDepth

        public int getMaxDepth()
        Gte the maximum depth (read count) of any genotype used in the accuracy calculation
        Returns:
        The maximum depth