예제 #1
0
파일: PhasingUtils.java 프로젝트: nh13/gatk
  static boolean someSampleHasDoubleNonReferenceAllele(VariantContext vc1, VariantContext vc2) {
    for (final Genotype gt1 : vc1.getGenotypes()) {
      Genotype gt2 = vc2.getGenotype(gt1.getSampleName());

      List<Allele> site1Alleles = gt1.getAlleles();
      List<Allele> site2Alleles = gt2.getAlleles();

      Iterator<Allele> all2It = site2Alleles.iterator();
      for (Allele all1 : site1Alleles) {
        Allele all2 = all2It.next(); // this is OK, since allSamplesAreMergeable()

        if (all1.isNonReference() && all2.isNonReference()) // corresponding alleles are alternate
        return true;
      }
    }

    return false;
  }
예제 #2
0
파일: PhasingUtils.java 프로젝트: nh13/gatk
  static boolean doubleAllelesSegregatePerfectlyAmongSamples(
      VariantContext vc1, VariantContext vc2) {
    // Check that Alleles at vc1 and at vc2 always segregate together in all samples (including
    // reference):
    Map<Allele, Allele> allele1ToAllele2 = new HashMap<Allele, Allele>();
    Map<Allele, Allele> allele2ToAllele1 = new HashMap<Allele, Allele>();

    // Note the segregation of the alleles for the reference genome:
    allele1ToAllele2.put(vc1.getReference(), vc2.getReference());
    allele2ToAllele1.put(vc2.getReference(), vc1.getReference());

    // Note the segregation of the alleles for each sample (and check that it is consistent with the
    // reference and all previous samples).
    for (final Genotype gt1 : vc1.getGenotypes()) {
      Genotype gt2 = vc2.getGenotype(gt1.getSampleName());

      List<Allele> site1Alleles = gt1.getAlleles();
      List<Allele> site2Alleles = gt2.getAlleles();

      Iterator<Allele> all2It = site2Alleles.iterator();
      for (Allele all1 : site1Alleles) {
        Allele all2 = all2It.next();

        Allele all1To2 = allele1ToAllele2.get(all1);
        if (all1To2 == null) allele1ToAllele2.put(all1, all2);
        else if (!all1To2.equals(all2)) // all1 segregates with two different alleles at site 2
        return false;

        Allele all2To1 = allele2ToAllele1.get(all2);
        if (all2To1 == null) allele2ToAllele1.put(all2, all1);
        else if (!all2To1.equals(all1)) // all2 segregates with two different alleles at site 1
        return false;
      }
    }

    return true;
  }
예제 #3
0
파일: PhasingUtils.java 프로젝트: nh13/gatk
  static VariantContext reallyMergeIntoMNP(
      VariantContext vc1, VariantContext vc2, ReferenceSequenceFile referenceFile) {
    int startInter = vc1.getEnd() + 1;
    int endInter = vc2.getStart() - 1;
    byte[] intermediateBases = null;
    if (startInter <= endInter) {
      intermediateBases =
          referenceFile.getSubsequenceAt(vc1.getChr(), startInter, endInter).getBases();
      StringUtil.toUpperCase(intermediateBases);
    }
    MergedAllelesData mergeData =
        new MergedAllelesData(
            intermediateBases, vc1, vc2); // ensures that the reference allele is added

    GenotypesContext mergedGenotypes = GenotypesContext.create();
    for (final Genotype gt1 : vc1.getGenotypes()) {
      Genotype gt2 = vc2.getGenotype(gt1.getSampleName());

      List<Allele> site1Alleles = gt1.getAlleles();
      List<Allele> site2Alleles = gt2.getAlleles();

      List<Allele> mergedAllelesForSample = new LinkedList<Allele>();

      /* NOTE: Since merged alleles are added to mergedAllelesForSample in the SAME order as in the input VC records,
        we preserve phase information (if any) relative to whatever precedes vc1:
      */
      Iterator<Allele> all2It = site2Alleles.iterator();
      for (Allele all1 : site1Alleles) {
        Allele all2 = all2It.next(); // this is OK, since allSamplesAreMergeable()

        Allele mergedAllele = mergeData.ensureMergedAllele(all1, all2);
        mergedAllelesForSample.add(mergedAllele);
      }

      double mergedGQ = Math.max(gt1.getLog10PError(), gt2.getLog10PError());
      Set<String> mergedGtFilters =
          new HashSet<
              String>(); // Since gt1 and gt2 were unfiltered, the Genotype remains unfiltered

      Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
      PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
      if (phaseQual.PQ != null) mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);

      Genotype mergedGt =
          new Genotype(
              gt1.getSampleName(),
              mergedAllelesForSample,
              mergedGQ,
              mergedGtFilters,
              mergedGtAttribs,
              phaseQual.isPhased);
      mergedGenotypes.add(mergedGt);
    }

    String mergedName = mergeVariantContextNames(vc1.getSource(), vc2.getSource());
    double mergedLog10PError = Math.min(vc1.getLog10PError(), vc2.getLog10PError());
    Set<String> mergedFilters =
        new HashSet<
            String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
    Map<String, Object> mergedAttribs = mergeVariantContextAttributes(vc1, vc2);

    // ids
    List<String> mergedIDs = new ArrayList<String>();
    if (vc1.hasID()) mergedIDs.add(vc1.getID());
    if (vc2.hasID()) mergedIDs.add(vc2.getID());
    String mergedID =
        mergedIDs.isEmpty()
            ? VCFConstants.EMPTY_ID_FIELD
            : Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);

    VariantContextBuilder mergedBuilder =
        new VariantContextBuilder(
                mergedName,
                vc1.getChr(),
                vc1.getStart(),
                vc2.getEnd(),
                mergeData.getAllMergedAlleles())
            .id(mergedID)
            .genotypes(mergedGenotypes)
            .log10PError(mergedLog10PError)
            .filters(mergedFilters)
            .attributes(mergedAttribs);
    VariantContextUtils.calculateChromosomeCounts(mergedBuilder, true);
    return mergedBuilder.make();
  }