Example #1
0
  public Map<String, Object> annotate(
      final RefMetaDataTracker tracker,
      final AnnotatorCompatible walker,
      final ReferenceContext ref,
      final Map<String, AlignmentContext> stratifiedContexts,
      final VariantContext vc,
      final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {

    int run;
    if (vc.isMixed()) {
      Map<String, Object> map = new HashMap<String, Object>();
      map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
      return map;

    } else if (vc.isIndel()) {
      String type = "";
      if (!vc.isBiallelic()) type = "MULTIALLELIC_INDEL";
      else {
        if (vc.isSimpleInsertion()) type = "INS.";
        else if (vc.isSimpleDeletion()) type = "DEL.";
        else type = "OTHER.";
        ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
        for (int k : inds) {
          type = type + IndelUtils.getIndelClassificationName(k) + ".";
        }
      }
      Map<String, Object> map = new HashMap<String, Object>();
      map.put(getKeyNames().get(0), String.format("%s", type));
      return map;

    } else {
      return null;
    }
  }
Example #2
0
  public String update1(
      VariantContext vc1,
      RefMetaDataTracker tracker,
      ReferenceContext ref,
      AlignmentContext context) {
    nCalledLoci++;

    // Note from Eric:
    // This is really not correct.  What we really want here is a polymorphic vs. monomorphic count
    // (i.e. on the Genotypes).
    // So in order to maintain consistency with the previous implementation (and the intention of
    // the original author), I've
    // added in a proxy check for monomorphic status here.
    // Protect against case when vc only as no-calls too - can happen if we strafity by sample and
    // sample as a single no-call.
    if (vc1.isMonomorphicInSamples()) {
      nRefLoci++;
    } else {
      switch (vc1.getType()) {
        case NO_VARIATION:
          // shouldn't get here
          break;
        case SNP:
          nVariantLoci++;
          nSNPs++;
          if (vc1.getAttributeAsBoolean("ISSINGLETON", false)) nSingletons++;
          break;
        case MNP:
          nVariantLoci++;
          nMNPs++;
          if (vc1.getAttributeAsBoolean("ISSINGLETON", false)) nSingletons++;
          break;
        case INDEL:
          nVariantLoci++;
          if (vc1.isSimpleInsertion()) nInsertions++;
          else if (vc1.isSimpleDeletion()) nDeletions++;
          else nComplex++;
          break;
        case MIXED:
          nVariantLoci++;
          nMixed++;
          break;
        case SYMBOLIC:
          nSymbolic++;
          break;
        default:
          throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
      }
    }

    String refStr = vc1.getReference().getBaseString().toUpperCase();

    String aaStr =
        vc1.hasAttribute("ANCESTRALALLELE")
            ? vc1.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase()
            : null;
    //        if (aaStr.equals(".")) {
    //            aaStr = refStr;
    //        }

    // ref  aa  alt  class
    // A    C   A    der homozygote
    // A    C   C    anc homozygote

    // A    A   A    ref homozygote
    // A    A   C
    // A    C   A
    // A    C   C

    for (final Genotype g : vc1.getGenotypes()) {
      final String altStr =
          vc1.getAlternateAlleles().size() > 0
              ? vc1.getAlternateAllele(0).getBaseString().toUpperCase()
              : null;

      switch (g.getType()) {
        case NO_CALL:
          nNoCalls++;
          break;
        case HOM_REF:
          nHomRef++;

          if (aaStr != null && altStr != null && !refStr.equalsIgnoreCase(aaStr)) {
            nHomDerived++;
          }

          break;
        case HET:
          nHets++;
          break;
        case HOM_VAR:
          nHomVar++;

          if (aaStr != null && altStr != null && !altStr.equalsIgnoreCase(aaStr)) {
            nHomDerived++;
          }

          break;
        case MIXED:
          break;
        default:
          throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
      }
    }

    return null; // we don't capture any interesting sites
  }