コード例 #1
0
ファイル: SelectVariants.java プロジェクト: singerma/gatk
  /**
   * 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;
  }
  /**
   * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority
   * order, if provided. If uniqifySamples is true, the priority order is ignored and names are
   * created by concatenating the VC name with the sample name
   *
   * @param genomeLocParser loc parser
   * @param unsortedVCs collection of unsorted VCs
   * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
   * @param filteredRecordMergeType merge type for filtered records
   * @param genotypeMergeOptions merge option for genotypes
   * @param annotateOrigin should we annotate the set it came from?
   * @param printMessages should we print messages?
   * @param setKey the key name of the set
   * @param filteredAreUncalled are filtered records uncalled?
   * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count?
   * @return new VariantContext representing the merge of unsortedVCs
   */
  public static VariantContext simpleMerge(
      final GenomeLocParser genomeLocParser,
      final Collection<VariantContext> unsortedVCs,
      final List<String> priorityListOfVCs,
      final FilteredRecordMergeType filteredRecordMergeType,
      final GenotypeMergeType genotypeMergeOptions,
      final boolean annotateOrigin,
      final boolean printMessages,
      final String setKey,
      final boolean filteredAreUncalled,
      final boolean mergeInfoWithMaxAC) {
    if (unsortedVCs == null || unsortedVCs.size() == 0) return null;

    if (annotateOrigin && priorityListOfVCs == null)
      throw new IllegalArgumentException(
          "Cannot merge calls and annotate their origins without a complete priority list of VariantContexts");

    if (genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE)
      verifyUniqueSampleNames(unsortedVCs);

    List<VariantContext> prepaddedVCs =
        sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions);
    // Make sure all variant contexts are padded with reference base in case of indels if necessary
    List<VariantContext> VCs = new ArrayList<VariantContext>();

    for (VariantContext vc : prepaddedVCs) {
      // also a reasonable place to remove filtered calls, if needed
      if (!filteredAreUncalled || vc.isNotFiltered())
        VCs.add(createVariantContextWithPaddedAlleles(vc, false));
    }
    if (VCs.size() == 0) // everything is filtered out and we're filteredAreUncalled
    return null;

    // establish the baseline info from the first VC
    final VariantContext first = VCs.get(0);
    final String name = first.getSource();
    final Allele refAllele = determineReferenceAllele(VCs);

    final Set<Allele> alleles = new LinkedHashSet<Allele>();
    final Set<String> filters = new TreeSet<String>();
    final Map<String, Object> attributes = new TreeMap<String, Object>();
    final Set<String> inconsistentAttributes = new HashSet<String>();
    final Set<String> variantSources =
        new HashSet<
            String>(); // contains the set of sources we found in our set of VCs that are variant
    final Set<String> rsIDs = new LinkedHashSet<String>(1); // most of the time there's one id

    GenomeLoc loc = getLocation(genomeLocParser, first);
    int depth = 0;
    int maxAC = -1;
    final Map<String, Object> attributesWithMaxAC = new TreeMap<String, Object>();
    double log10PError = 1;
    VariantContext vcWithMaxAC = null;
    GenotypesContext genotypes = GenotypesContext.create();

    // counting the number of filtered and variant VCs
    int nFiltered = 0;

    boolean remapped = false;

    // cycle through and add info from the other VCs, making sure the loc/reference matches

    for (VariantContext vc : VCs) {
      if (loc.getStart() != vc.getStart()) // || !first.getReference().equals(vc.getReference()) )
      throw new ReviewedStingException(
            "BUG: attempting to merge VariantContexts with different start sites: first="
                + first.toString()
                + " second="
                + vc.toString());

      if (getLocation(genomeLocParser, vc).size() > loc.size())
        loc = getLocation(genomeLocParser, vc); // get the longest location

      nFiltered += vc.isFiltered() ? 1 : 0;
      if (vc.isVariant()) variantSources.add(vc.getSource());

      AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles);
      remapped = remapped || alleleMapping.needsRemapping();

      alleles.addAll(alleleMapping.values());

      mergeGenotypes(
          genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY);

      log10PError = Math.min(log10PError, vc.isVariant() ? vc.getLog10PError() : 1);

      filters.addAll(vc.getFilters());

      //
      // add attributes
      //
      // special case DP (add it up) and ID (just preserve it)
      //
      if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
        depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
      if (vc.hasID()) rsIDs.add(vc.getID());
      if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
        String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null);
        // lets see if the string contains a , separator
        if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) {
          List<String> alleleCountArray =
              Arrays.asList(
                  rawAlleleCounts
                      .substring(1, rawAlleleCounts.length() - 1)
                      .split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR));
          for (String alleleCount : alleleCountArray) {
            final int ac = Integer.valueOf(alleleCount.trim());
            if (ac > maxAC) {
              maxAC = ac;
              vcWithMaxAC = vc;
            }
          }
        } else {
          final int ac = Integer.valueOf(rawAlleleCounts);
          if (ac > maxAC) {
            maxAC = ac;
            vcWithMaxAC = vc;
          }
        }
      }

      for (Map.Entry<String, Object> p : vc.getAttributes().entrySet()) {
        String key = p.getKey();
        // if we don't like the key already, don't go anywhere
        if (!inconsistentAttributes.contains(key)) {
          boolean alreadyFound = attributes.containsKey(key);
          Object boundValue = attributes.get(key);
          boolean boundIsMissingValue =
              alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4);

          if (alreadyFound && !boundValue.equals(p.getValue()) && !boundIsMissingValue) {
            // we found the value but we're inconsistent, put it in the exclude list
            // System.out.printf("Inconsistent INFO values: %s => %s and %s%n", key, boundValue,
            // p.getValue());
            inconsistentAttributes.add(key);
            attributes.remove(key);
          } else if (!alreadyFound || boundIsMissingValue) { // no value
            // if ( vc != first ) System.out.printf("Adding key %s => %s%n", p.getKey(),
            // p.getValue());
            attributes.put(key, p.getValue());
          }
        }
      }
    }

    // if we have more alternate alleles in the merged VC than in one or more of the
    // original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well
    // as allele-dependent attributes like AC,AF
    for (VariantContext vc : VCs) {
      if (vc.alleles.size() == 1) continue;
      if (hasPLIncompatibleAlleles(alleles, vc.alleles)) {
        if (!genotypes.isEmpty())
          logger.warn(
              String.format(
                  "Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
                  genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
        genotypes = stripPLs(genotypes);
        // this will remove stale AC,AF attributed from vc
        calculateChromosomeCounts(vc, attributes, true);
        break;
      }
    }

    // take the VC with the maxAC and pull the attributes into a modifiable map
    if (mergeInfoWithMaxAC && vcWithMaxAC != null) {
      attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes());
    }

    // if at least one record was unfiltered and we want a union, clear all of the filters
    if ((filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
            && nFiltered != VCs.size())
        || filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL) filters.clear();

    if (annotateOrigin) { // we care about where the call came from
      String setValue;
      if (nFiltered == 0
          && variantSources.size() == priorityListOfVCs.size()) // nothing was unfiltered
      setValue = MERGE_INTERSECTION;
      else if (nFiltered == VCs.size()) // everything was filtered out
      setValue = MERGE_FILTER_IN_ALL;
      else if (variantSources.isEmpty()) // everyone was reference
      setValue = MERGE_REF_IN_ALL;
      else {
        LinkedHashSet<String> s = new LinkedHashSet<String>();
        for (VariantContext vc : VCs)
          if (vc.isVariant())
            s.add(vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource());
        setValue = Utils.join("-", s);
      }

      if (setKey != null) {
        attributes.put(setKey, setValue);
        if (mergeInfoWithMaxAC && vcWithMaxAC != null) {
          attributesWithMaxAC.put(setKey, vcWithMaxAC.getSource());
        }
      }
    }

    if (depth > 0) attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));

    final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);

    final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID);
    builder.loc(loc.getContig(), loc.getStart(), loc.getStop());
    builder.alleles(alleles);
    builder.genotypes(genotypes);
    builder.log10PError(log10PError);
    builder.filters(filters).attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes);

    // Trim the padded bases of all alleles if necessary
    VariantContext merged = createVariantContextWithTrimmedAlleles(builder.make());
    if (printMessages && remapped) System.out.printf("Remapped => %s%n", merged);
    return merged;
  }
コード例 #3
0
ファイル: PhasingUtils.java プロジェクト: 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();
  }