/**
* Update the attributes of the attributes map given the VariantContext to reflect the proper
* chromosome-based VCF tags
*
* @param vc the VariantContext
* @param attributes the attributes map to populate; must not be null; may contain old values
* @param removeStaleValues should we remove stale values from the mapping?
* @return the attributes map provided as input, returned for programming convenience
*/
public static Map<String, Object> calculateChromosomeCounts(
VariantContext vc, Map<String, Object> attributes, boolean removeStaleValues) {
final int AN = vc.getCalledChrCount();
// if everyone is a no-call, remove the old attributes if requested
if (AN == 0 && removeStaleValues) {
if (attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY))
attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
if (attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY))
attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
if (attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY))
attributes.remove(VCFConstants.ALLELE_NUMBER_KEY);
return attributes;
}
if (vc.hasGenotypes()) {
attributes.put(VCFConstants.ALLELE_NUMBER_KEY, AN);
// if there are alternate alleles, record the relevant tags
if (vc.getAlternateAlleles().size() > 0) {
final ArrayList<String> alleleFreqs = new ArrayList<String>();
final ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
for (Allele allele : vc.getAlternateAlleles()) {
int altChromosomes = vc.getCalledChrCount(allele);
alleleCounts.add(altChromosomes);
if (AN == 0) {
alleleFreqs.add("0.0");
} else {
// todo -- this is a performance problem
final String freq =
String.format(
makePrecisionFormatStringFromDenominatorValue((double) AN),
((double) altChromosomes / (double) AN));
alleleFreqs.add(freq);
}
}
attributes.put(
VCFConstants.ALLELE_COUNT_KEY,
alleleCounts.size() == 1 ? alleleCounts.get(0) : alleleCounts);
attributes.put(
VCFConstants.ALLELE_FREQUENCY_KEY,
alleleFreqs.size() == 1 ? alleleFreqs.get(0) : alleleFreqs);
} else {
attributes.put(VCFConstants.ALLELE_COUNT_KEY, 0);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
}
}
return attributes;
}
public static double computeHardyWeinbergPvalue(VariantContext vc) {
if (vc.getCalledChrCount() == 0) return 0.0;
return HardyWeinbergCalculation.hwCalculate(
vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount());
}