Class VariantStats

    • Field Detail

      • CHANGE_SEPARATOR

        public static final java.lang.String CHANGE_SEPARATOR
        See Also:
        Constant Field Values
    • Constructor Detail

      • VariantStats

        public VariantStats​(Genome genome)
    • Method Detail

      • getBases

        public char[] getBases()
      • getBasesChangesColor

        public java.lang.String getBasesChangesColor​(java.lang.String oldBase,
                                                     java.lang.String newBase)
        Background color used for base change table
      • getBasesChangesCount

        public long getBasesChangesCount​(java.lang.String oldBase,
                                         java.lang.String newBase)
      • getChangeTypeLength

        public int getChangeTypeLength()
      • getChromosomeLength

        public int getChromosomeLength​(java.lang.String chromoName)
        Choromosome length
        Parameters:
        chromoName -
        Returns:
      • getChromosomeNamesEffective

        public java.util.List<java.lang.String> getChromosomeNamesEffective()
        A list of chromosomes that had at least one change Note: Chromosome names are sorted.
        Returns:
      • getChrPosStats

        public ChrPosStats getChrPosStats​(java.lang.String chrName)
      • getChrPosStatsChartUrl

        public java.lang.String getChrPosStatsChartUrl​(java.lang.String chrName)
      • getCount

        public long getCount()
        Total number of variants
        Returns:
      • getCountByChangeType

        public CountByType getCountByChangeType()
        Number of variants by type
        Returns:
      • getCountByChromosome

        public int getCountByChromosome​(java.lang.String chromoName)
        Number of changes by chromosome
        Parameters:
        chromoName -
        Returns:
      • getCountNonEmptyId

        public long getCountNonEmptyId()
      • getCountNonVariants

        public long getCountNonVariants()
      • getGenomeLen

        public long getGenomeLen()
        Genome length
        Returns:
      • getGenomeLenEffective

        public long getGenomeLenEffective()
        Genome effective length: The sum of length of every chromosome that had a change (e.g. If there was no SNP in chromosome Y, then it doesn't count in the effective length)
        Returns:
      • getIndelLen

        public IntStats getIndelLen()
      • getIndelLenHistoUrl

        public java.lang.String getIndelLenHistoUrl()
      • getKnownRatio

        public double getKnownRatio()
        Ratio of known variants (the one with a non-empty ID) and total variants
      • getRateOfChange

        public long getRateOfChange()
        Rate of change
        Returns:
      • getRateOfChangeByChromosome

        public int getRateOfChangeByChromosome​(java.lang.String chromoName)
        Rate of change by chromosome
        Parameters:
        chromoName -
        Returns: