Exemple #1
0
 public int getNumberOfSamplesForEvaluation() {
   if (sampleNamesForEvaluation != null && !sampleNamesForEvaluation.isEmpty())
     return sampleNamesForEvaluation.size();
   else {
     return numSamplesFromArgument;
   }
 }
Exemple #2
0
  /**
   * Helper method to subset a VC record, modifying some metadata stored in the INFO field (i.e. AN,
   * AC, AF).
   *
   * @param vc the VariantContext record to subset
   * @param samples the samples to extract
   * @return the subsetted VariantContext
   */
  private VariantContext subsetRecord(VariantContext vc, Set<String> samples) {
    if (samples == null || samples.isEmpty()) return vc;

    ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
    for (Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet()) {
      if (samples.contains(genotypePair.getKey())) genotypes.add(genotypePair.getValue());
    }

    VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());

    // if we have fewer alternate alleles in the selected VC than in the original VC, we need to
    // strip out the GL/PLs (because they are no longer accurate)
    if (vc.getAlleles().size() != sub.getAlleles().size())
      sub = VariantContext.modifyGenotypes(sub, VariantContextUtils.stripPLs(vc.getGenotypes()));

    HashMap<String, Object> attributes = new HashMap<String, Object>(sub.getAttributes());

    int depth = 0;
    for (String sample : sub.getSampleNames()) {
      Genotype g = sub.getGenotype(sample);

      if (g.isNotFiltered() && g.isCalled()) {

        String dp = (String) g.getAttribute("DP");
        if (dp != null
            && !dp.equals(VCFConstants.MISSING_DEPTH_v3)
            && !dp.equals(VCFConstants.MISSING_VALUE_v4)) {
          depth += Integer.valueOf(dp);
        }
      }
    }

    if (KEEP_ORIGINAL_CHR_COUNTS) {
      if (attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY))
        attributes.put("AC_Orig", attributes.get(VCFConstants.ALLELE_COUNT_KEY));
      if (attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY))
        attributes.put("AF_Orig", attributes.get(VCFConstants.ALLELE_FREQUENCY_KEY));
      if (attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY))
        attributes.put("AN_Orig", attributes.get(VCFConstants.ALLELE_NUMBER_KEY));
    }

    VariantContextUtils.calculateChromosomeCounts(sub, attributes, false);
    attributes.put("DP", depth);

    sub = VariantContext.modifyAttributes(sub, attributes);

    return sub;
  }