Constructor Detail

• GenotypeConcordanceCounts

  public GenotypeConcordanceCounts()

Method Detail

• increment

  public void increment​(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)

  Increments a count for the truth/call state tuple.

  Parameters:

  truthAndCallStates -

• increment

  public void increment​(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates,
                        double count)

• getCounterSize

  public double getCounterSize()

• validateCountsAgainstScheme

  public void validateCountsAgainstScheme​(GenotypeConcordanceScheme scheme)

  Validates that there are no counts for NA states in the underlying scheme

• calculateGenotypeConcordance

  public double calculateGenotypeConcordance​(GenotypeConcordanceScheme scheme,
                                             boolean missingSitesFlag)

  Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.

• calculateNonRefGenotypeConcordance

  public double calculateNonRefGenotypeConcordance​(GenotypeConcordanceScheme scheme,
                                                   boolean missingSitesFlag)

  Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.

• getSensitivity

  public double getSensitivity​(GenotypeConcordanceScheme scheme,
                               GenotypeConcordanceStates.TruthState[] truthStateArray)

  Returns the sensitivity defined by the scheme across the subset of truth states.

• Ppv

  public double Ppv​(GenotypeConcordanceScheme scheme,
                    GenotypeConcordanceStates.CallState[] callStateList)

  Returns the PPV defined by the scheme across the subset of call states.

• getSpecificity

  public double getSpecificity​(GenotypeConcordanceScheme scheme,
                               GenotypeConcordanceStates.TruthState[] truthStateArray)

  Returns the specificity defined by the scheme across the subset of truth states.

• getCount

  public long getCount​(GenotypeConcordanceStates.TruthState truthState,
                       GenotypeConcordanceStates.CallState callState)

  Returns the count defined by the truth state set and call state set.

• getCount

  public long getCount​(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates)

  Returns the count defined by the truth state set and call state set.

• isVar

  public boolean isVar​(GenotypeConcordanceStates.TruthState truthState,
                       GenotypeConcordanceStates.CallState callState)

  Returns true if EITHER the truth or call state is a VAR. Used for calculating non ref genotype concordance.

• isMissing

  public boolean isMissing​(GenotypeConcordanceStates.TruthState truthState,
                           GenotypeConcordanceStates.CallState callState)

  Returns true if EITHER the truth or call state is MISSING. Used for calculating genotype concordance and non-ref genotype concordance when the GA4GH scheme is used.

• getSum

  public long getSum​(Set<GenotypeConcordanceStates.TruthState> truthStateSet,
                     Set<GenotypeConcordanceStates.CallState> callStateSet)

  Returns the sum of all pairs of tuples defined by the truth state set and call state set.

• getSum

  public long getSum()

  Returns the sum of all pairs of tuples defined by the truth state set and call state set.

• getContingencyStateCounts

  public Map<GenotypeConcordanceStates.ContingencyState,​Long> getContingencyStateCounts​(GenotypeConcordanceScheme scheme)

  Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.