@Test
  public void substractComplexExample() {
    GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 20);
    mSortedSet.add(e);

    GenomeLoc r1 = genomeLocParser.createGenomeLoc(contigOneName, 3, 5);
    GenomeLoc r2 = genomeLocParser.createGenomeLoc(contigOneName, 10, 12);
    GenomeLoc r3 = genomeLocParser.createGenomeLoc(contigOneName, 16, 18);
    GenomeLocSortedSet toExclude =
        new GenomeLocSortedSet(genomeLocParser, Arrays.asList(r1, r2, r3));

    GenomeLocSortedSet remaining = mSortedSet.subtractRegions(toExclude);
    //        logger.debug("Initial   " + mSortedSet);
    //        logger.debug("Exclude   " + toExclude);
    //        logger.debug("Remaining " + remaining);

    assertEquals(mSortedSet.coveredSize(), 20);
    assertEquals(toExclude.coveredSize(), 9);
    assertEquals(remaining.coveredSize(), 11);

    Iterator<GenomeLoc> it = remaining.iterator();
    GenomeLoc p1 = it.next();
    GenomeLoc p2 = it.next();
    GenomeLoc p3 = it.next();
    GenomeLoc p4 = it.next();

    assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 1, 2), p1);
    assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 6, 9), p2);
    assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 13, 15), p3);
    assertEquals(genomeLocParser.createGenomeLoc(contigOneName, 19, 20), p4);
  }
  @Test
  public void testSizeBeforeLoc() {
    GenomeLoc r1 = genomeLocParser.createGenomeLoc(contigOneName, 3, 5);
    GenomeLoc r2 = genomeLocParser.createGenomeLoc(contigOneName, 10, 12);
    GenomeLoc r3 = genomeLocParser.createGenomeLoc(contigOneName, 16, 18);
    mSortedSet.addAll(Arrays.asList(r1, r2, r3));

    testSizeBeforeLocX(2, 0);
    testSizeBeforeLocX(3, 0);
    testSizeBeforeLocX(4, 1);
    testSizeBeforeLocX(5, 2);
    testSizeBeforeLocX(6, 3);

    testSizeBeforeLocX(10, 3);
    testSizeBeforeLocX(11, 4);
    testSizeBeforeLocX(12, 5);
    testSizeBeforeLocX(13, 6);
    testSizeBeforeLocX(15, 6);

    testSizeBeforeLocX(16, 6);
    testSizeBeforeLocX(17, 7);
    testSizeBeforeLocX(18, 8);
    testSizeBeforeLocX(19, 9);
    testSizeBeforeLocX(50, 9);
    testSizeBeforeLocX(50, (int) mSortedSet.coveredSize());
  }
 @Test(expectedExceptions = IllegalArgumentException.class)
 public void addThrowsException() {
   assertTrue(mSortedSet.size() == 0);
   GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 1, 50);
   mSortedSet.add(g);
   GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
   mSortedSet.add(f);
 }
Esempio n. 4
0
 /**
  * create a list of genomic locations, given a reference sequence
  *
  * @param dict the sequence dictionary to create a collection from
  * @return the GenomeLocSet of all references sequences as GenomeLoc's
  */
 public static GenomeLocSortedSet createSetFromSequenceDictionary(SAMSequenceDictionary dict) {
   GenomeLocParser parser = new GenomeLocParser(dict);
   GenomeLocSortedSet returnSortedSet = new GenomeLocSortedSet(parser);
   for (SAMSequenceRecord record : dict.getSequences()) {
     returnSortedSet.add(
         parser.createGenomeLoc(record.getSequenceName(), 1, record.getSequenceLength()));
   }
   return returnSortedSet;
 }
 @Test
 public void addRegion() {
   assertTrue(mSortedSet.size() == 0);
   GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 1, 50);
   mSortedSet.add(g);
   GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
   mSortedSet.addRegion(f);
   assertTrue(mSortedSet.size() == 1);
 }
 @Test
 public void deleteAllByRegion() {
   GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 100);
   mSortedSet.add(e);
   for (int x = 1; x < 101; x++) {
     GenomeLoc del = genomeLocParser.createGenomeLoc(contigOneName, x, x);
     mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, del));
   }
   assertTrue(mSortedSet.isEmpty());
 }
 @Test
 public void addRegionsOutOfOrder() {
   final String contigTwoName = header.getSequenceDictionary().getSequence(2).getSequenceName();
   assertTrue(mSortedSet.size() == 0);
   GenomeLoc g = genomeLocParser.createGenomeLoc(contigTwoName, 1, 50);
   mSortedSet.add(g);
   GenomeLoc f = genomeLocParser.createGenomeLoc(contigOneName, 30, 80);
   mSortedSet.addRegion(f);
   assertTrue(mSortedSet.size() == 2);
   assertTrue(mSortedSet.toList().get(0).getContig().equals(contigOneName));
   assertTrue(mSortedSet.toList().get(1).getContig().equals(contigTwoName));
 }
 @Test
 public void deleteSomeByRegion() {
   GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 1, 100);
   mSortedSet.add(e);
   for (int x = 1; x < 50; x++) {
     GenomeLoc del = genomeLocParser.createGenomeLoc(contigOneName, x, x);
     mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, del));
   }
   assertTrue(!mSortedSet.isEmpty());
   assertTrue(mSortedSet.size() == 1);
   GenomeLoc loc = mSortedSet.iterator().next();
   assertTrue(loc.getStop() == 100);
   assertTrue(loc.getStart() == 50);
 }
 @Test
 public void mergingOverlappingAbove() {
   GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 0, 50);
   GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 49, 100);
   assertTrue(mSortedSet.size() == 0);
   mSortedSet.add(g);
   assertTrue(mSortedSet.size() == 1);
   mSortedSet.addRegion(e);
   assertTrue(mSortedSet.size() == 1);
   Iterator<GenomeLoc> iter = mSortedSet.iterator();
   GenomeLoc loc = iter.next();
   assertEquals(loc.getStart(), 0);
   assertEquals(loc.getStop(), 100);
   assertEquals(loc.getContigIndex(), 1);
 }
Esempio n. 10
0
 @Test
 public void testAdd() {
   GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 0, 0);
   assertTrue(mSortedSet.size() == 0);
   mSortedSet.add(g);
   assertTrue(mSortedSet.size() == 1);
 }
Esempio n. 11
0
 @Test(expectedExceptions = IllegalArgumentException.class)
 public void testAddDuplicate() {
   assertTrue(mSortedSet.size() == 0);
   GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 0, 0);
   mSortedSet.add(g);
   assertTrue(mSortedSet.size() == 1);
   mSortedSet.add(g);
 }
Esempio n. 12
0
 /**
  * return a deep copy of this collection.
  *
  * @return a new GenomeLocSortedSet, identical to the current GenomeLocSortedSet.
  */
 public GenomeLocSortedSet clone() {
   GenomeLocSortedSet ret = new GenomeLocSortedSet(genomeLocParser);
   for (GenomeLoc loc : this.mArray) {
     // ensure a deep copy
     ret.mArray.add(
         genomeLocParser.createGenomeLoc(loc.getContig(), loc.getStart(), loc.getStop()));
   }
   return ret;
 }
Esempio n. 13
0
  @Test
  public void deleteSuperRegion() {
    GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 10, 20);
    GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 70, 100);
    mSortedSet.add(g);
    mSortedSet.addRegion(e);
    assertTrue(mSortedSet.size() == 2);
    // now delete a region
    GenomeLoc d = genomeLocParser.createGenomeLoc(contigOneName, 15, 75);
    mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, d));
    Iterator<GenomeLoc> iter = mSortedSet.iterator();
    GenomeLoc loc = iter.next();
    assertTrue(loc.getStart() == 10);
    assertTrue(loc.getStop() == 14);
    assertTrue(loc.getContigIndex() == 1);

    loc = iter.next();
    assertTrue(loc.getStart() == 76);
    assertTrue(loc.getStop() == 100);
    assertTrue(loc.getContigIndex() == 1);
  }
Esempio n. 14
0
  @DataProvider(name = "GetOverlapping")
  public Object[][] makeGetOverlappingTest() throws Exception {
    final GenomeLocParser genomeLocParser =
        new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));

    List<Object[]> tests = new ArrayList<Object[]>();

    final GenomeLoc prev1 = genomeLocParser.createGenomeLoc("19", 1, 10);
    final GenomeLoc prev2 = genomeLocParser.createGenomeLoc("19", 20, 50);
    final GenomeLoc post1 = genomeLocParser.createGenomeLoc("21", 1, 10);
    final GenomeLoc post2 = genomeLocParser.createGenomeLoc("21", 20, 50);

    final int chr20Length = genomeLocParser.getContigs().getSequence("20").getSequenceLength();
    for (final int regionStart : Arrays.asList(1, 10, chr20Length - 10, chr20Length)) {
      for (final int regionSize : Arrays.asList(1, 10, 100)) {
        final GenomeLoc region =
            genomeLocParser.createGenomeLocOnContig("20", regionStart, regionStart + regionSize);
        final GenomeLoc spanning =
            genomeLocParser.createGenomeLocOnContig("20", regionStart - 10, region.getStop() + 10);
        final GenomeLoc before_into =
            genomeLocParser.createGenomeLocOnContig("20", regionStart - 10, regionStart + 1);
        final GenomeLoc middle =
            genomeLocParser.createGenomeLocOnContig("20", regionStart + 1, regionStart + 2);
        final GenomeLoc middle_past =
            genomeLocParser.createGenomeLocOnContig(
                "20", region.getStop() - 1, region.getStop() + 10);

        final List<GenomeLoc> potentials = new LinkedList<GenomeLoc>();
        potentials.add(region);
        if (spanning != null) potentials.add(spanning);
        if (before_into != null) potentials.add(before_into);
        if (middle != null) potentials.add(middle);
        if (middle_past != null) potentials.add(middle_past);

        for (final int n : Arrays.asList(1, 2, 3)) {
          for (final List<GenomeLoc> regions : Utils.makePermutations(potentials, n, false)) {
            tests.add(new Object[] {new GenomeLocSortedSet(genomeLocParser, regions), region});
            tests.add(
                new Object[] {
                  new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1)), region
                });
            tests.add(
                new Object[] {
                  new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1, prev2)),
                  region
                });
            tests.add(
                new Object[] {
                  new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, post1)), region
                });
            tests.add(
                new Object[] {
                  new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, post1, post2)),
                  region
                });
            tests.add(
                new Object[] {
                  new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1, post1)),
                  region
                });
            tests.add(
                new Object[] {
                  new GenomeLocSortedSet(
                      genomeLocParser, Utils.append(regions, prev1, prev2, post1, post2)),
                  region
                });
          }
        }
      }
    }

    return tests.toArray(new Object[][] {});
  }
Esempio n. 15
0
 private void testSizeBeforeLocX(int pos, int size) {
   GenomeLoc test = genomeLocParser.createGenomeLoc(contigOneName, pos, pos);
   assertEquals(
       mSortedSet.sizeBeforeLoc(test), size, String.format("X pos=%d size=%d", pos, size));
 }
Esempio n. 16
0
  @Test
  public void overlap() {
    for (int i = 1; i < 6; i++) {
      final int start = i * 10;
      mSortedSet.add(genomeLocParser.createGenomeLoc(contigOneName, start, start + 1));
    }

    // test matches in and around interval
    assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 9, 9)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 10, 10)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 11, 11)));
    assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 12, 12)));

    // test matches spanning intervals
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 14, 20)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 11, 15)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 30, 40)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 51, 53)));

    // test miss
    assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 12, 19)));

    // test exact match after miss
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 40, 41)));

    // test matches at beginning of intervals
    assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 5, 6)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 0, 10)));

    // test matches at end of intervals
    assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 52, 53)));
    assertTrue(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 51, 53)));
    assertFalse(mSortedSet.overlaps(genomeLocParser.createGenomeLoc(contigOneName, 52, 53)));
  }
Esempio n. 17
0
  /**
   * Read in a list of ExactCall objects from reader, keeping only those with starts in startsToKeep
   * or all sites (if this is empty)
   *
   * @param reader a just-opened reader sitting at the start of the file
   * @param startsToKeep a list of start position of the calls to keep, or empty if all calls should
   *     be kept
   * @param parser a genome loc parser to create genome locs
   * @return a list of ExactCall objects in reader
   * @throws IOException
   */
  public static List<ExactCall> readExactLog(
      final BufferedReader reader, final List<Integer> startsToKeep, GenomeLocParser parser)
      throws IOException {
    if (reader == null) throw new IllegalArgumentException("reader cannot be null");
    if (startsToKeep == null) throw new IllegalArgumentException("startsToKeep cannot be null");
    if (parser == null) throw new IllegalArgumentException("GenomeLocParser cannot be null");

    List<ExactCall> calls = new LinkedList<ExactCall>();

    // skip the header line
    reader.readLine();

    // skip the first "type" line
    reader.readLine();

    while (true) {
      final VariantContextBuilder builder = new VariantContextBuilder();
      final List<Allele> alleles = new ArrayList<Allele>();
      final List<Genotype> genotypes = new ArrayList<Genotype>();
      final double[] posteriors = new double[2];
      final double[] priors = MathUtils.normalizeFromLog10(new double[] {0.5, 0.5}, true);
      final List<Integer> mle = new ArrayList<Integer>();
      final Map<Allele, Double> log10pNonRefByAllele = new HashMap<Allele, Double>();
      long runtimeNano = -1;

      GenomeLoc currentLoc = null;
      while (true) {
        final String line = reader.readLine();
        if (line == null) return calls;

        final String[] parts = line.split("\t");
        final GenomeLoc lineLoc = parser.parseGenomeLoc(parts[0]);
        final String variable = parts[1];
        final String key = parts[2];
        final String value = parts[3];

        if (currentLoc == null) currentLoc = lineLoc;

        if (variable.equals("type")) {
          if (startsToKeep.isEmpty() || startsToKeep.contains(currentLoc.getStart())) {
            builder.alleles(alleles);
            final int stop = currentLoc.getStart() + alleles.get(0).length() - 1;
            builder.chr(currentLoc.getContig()).start(currentLoc.getStart()).stop(stop);
            builder.genotypes(genotypes);
            final int[] mleInts = ArrayUtils.toPrimitive(mle.toArray(new Integer[] {}));
            final AFCalcResult result =
                new AFCalcResult(mleInts, 1, alleles, posteriors, priors, log10pNonRefByAllele);
            calls.add(new ExactCall(builder.make(), runtimeNano, result));
          }
          break;
        } else if (variable.equals("allele")) {
          final boolean isRef = key.equals("0");
          alleles.add(Allele.create(value, isRef));
        } else if (variable.equals("PL")) {
          final GenotypeBuilder gb = new GenotypeBuilder(key);
          gb.PL(GenotypeLikelihoods.fromPLField(value).getAsPLs());
          genotypes.add(gb.make());
        } else if (variable.equals("log10PosteriorOfAFEq0")) {
          posteriors[0] = Double.valueOf(value);
        } else if (variable.equals("log10PosteriorOfAFGt0")) {
          posteriors[1] = Double.valueOf(value);
        } else if (variable.equals("MLE")) {
          mle.add(Integer.valueOf(value));
        } else if (variable.equals("pNonRefByAllele")) {
          final Allele a = Allele.create(key);
          log10pNonRefByAllele.put(a, Double.valueOf(value));
        } else if (variable.equals("runtime.nano")) {
          runtimeNano = Long.valueOf(value);
        } else {
          // nothing to do
        }
      }
    }
  }
  /**
   * Main entry function to calculate genotypes of a given VC with corresponding GL's
   *
   * @param tracker Tracker
   * @param refContext Reference context
   * @param rawContext Raw context
   * @param stratifiedContexts Stratified alignment contexts
   * @param vc Input VC
   * @param model GL calculation model
   * @param inheritAttributesFromInputVC Output VC will contain attributes inherited from input vc
   * @return VC with assigned genotypes
   */
  public VariantCallContext calculateGenotypes(
      final RefMetaDataTracker tracker,
      final ReferenceContext refContext,
      final AlignmentContext rawContext,
      Map<String, AlignmentContext> stratifiedContexts,
      final VariantContext vc,
      final GenotypeLikelihoodsCalculationModel.Model model,
      final boolean inheritAttributesFromInputVC,
      final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap>
          perReadAlleleLikelihoodMap) {

    boolean limitedContext =
        tracker == null || refContext == null || rawContext == null || stratifiedContexts == null;

    // initialize the data for this thread if that hasn't been done yet
    if (afcm.get() == null) {
      afcm.set(AFCalcFactory.createAFCalc(UAC, N, logger));
    }

    // estimate our confidence in a reference call and return
    if (vc.getNSamples() == 0) {
      if (limitedContext) return null;
      return (UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES
          ? estimateReferenceConfidence(vc, stratifiedContexts, getTheta(model), false, 1.0)
          : generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext));
    }

    AFCalcResult AFresult = afcm.get().getLog10PNonRef(vc, getAlleleFrequencyPriors(model));

    // is the most likely frequency conformation AC=0 for all alternate alleles?
    boolean bestGuessIsRef = true;

    // determine which alternate alleles have AF>0
    final List<Allele> myAlleles = new ArrayList<Allele>(vc.getAlleles().size());
    final List<Integer> alleleCountsofMLE = new ArrayList<Integer>(vc.getAlleles().size());
    myAlleles.add(vc.getReference());
    for (int i = 0; i < AFresult.getAllelesUsedInGenotyping().size(); i++) {
      final Allele alternateAllele = AFresult.getAllelesUsedInGenotyping().get(i);
      if (alternateAllele.isReference()) continue;

      // we are non-ref if the probability of being non-ref > the emit confidence.
      // the emit confidence is phred-scaled, say 30 => 10^-3.
      // the posterior AF > 0 is log10: -5 => 10^-5
      // we are non-ref if 10^-5 < 10^-3 => -5 < -3
      final boolean isNonRef =
          AFresult.isPolymorphic(alternateAllele, UAC.STANDARD_CONFIDENCE_FOR_EMITTING / -10.0);

      // if the most likely AC is not 0, then this is a good alternate allele to use
      if (isNonRef) {
        myAlleles.add(alternateAllele);
        alleleCountsofMLE.add(AFresult.getAlleleCountAtMLE(alternateAllele));
        bestGuessIsRef = false;
      }
      // if in GENOTYPE_GIVEN_ALLELES mode, we still want to allow the use of a poor allele
      else if (UAC.GenotypingMode
          == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
        myAlleles.add(alternateAllele);
        alleleCountsofMLE.add(AFresult.getAlleleCountAtMLE(alternateAllele));
      }
    }

    final double PoFGT0 = Math.pow(10, AFresult.getLog10PosteriorOfAFGT0());

    // note the math.abs is necessary because -10 * 0.0 => -0.0 which isn't nice
    final double phredScaledConfidence =
        Math.abs(
            !bestGuessIsRef
                    || UAC.GenotypingMode
                        == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE
                            .GENOTYPE_GIVEN_ALLELES
                ? -10 * AFresult.getLog10PosteriorOfAFEq0()
                : -10 * AFresult.getLog10PosteriorOfAFGT0());

    // return a null call if we don't pass the confidence cutoff or the most likely allele frequency
    // is zero
    if (UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES
        && !passesEmitThreshold(phredScaledConfidence, bestGuessIsRef)) {
      // technically, at this point our confidence in a reference call isn't accurately estimated
      //  because it didn't take into account samples with no data, so let's get a better estimate
      return limitedContext
          ? null
          : estimateReferenceConfidence(vc, stratifiedContexts, getTheta(model), true, PoFGT0);
    }

    // start constructing the resulting VC
    final GenomeLoc loc = genomeLocParser.createGenomeLoc(vc);
    final VariantContextBuilder builder =
        new VariantContextBuilder(
            "UG_call", loc.getContig(), loc.getStart(), loc.getStop(), myAlleles);
    builder.log10PError(phredScaledConfidence / -10.0);
    if (!passesCallThreshold(phredScaledConfidence)) builder.filters(filter);

    // create the genotypes
    final GenotypesContext genotypes = afcm.get().subsetAlleles(vc, myAlleles, true, ploidy);
    builder.genotypes(genotypes);

    // print out stats if we have a writer
    if (verboseWriter != null && !limitedContext)
      printVerboseData(refContext.getLocus().toString(), vc, PoFGT0, phredScaledConfidence, model);

    // *** note that calculating strand bias involves overwriting data structures, so we do that
    // last
    final HashMap<String, Object> attributes = new HashMap<String, Object>();

    // inherit attributed from input vc if requested
    if (inheritAttributesFromInputVC) attributes.putAll(vc.getAttributes());
    // if the site was downsampled, record that fact
    if (!limitedContext && rawContext.hasPileupBeenDownsampled())
      attributes.put(VCFConstants.DOWNSAMPLED_KEY, true);

    if (UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED)
      attributes.put(NUMBER_OF_DISCOVERED_ALLELES_KEY, vc.getAlternateAlleles().size());

    // add the MLE AC and AF annotations
    if (alleleCountsofMLE.size() > 0) {
      attributes.put(VCFConstants.MLE_ALLELE_COUNT_KEY, alleleCountsofMLE);
      final int AN = builder.make().getCalledChrCount();
      final ArrayList<Double> MLEfrequencies = new ArrayList<Double>(alleleCountsofMLE.size());
      // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT
      // is ./. but the exact model may arbitrarily choose an AC>1)
      for (int AC : alleleCountsofMLE) MLEfrequencies.add(Math.min(1.0, (double) AC / (double) AN));
      attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies);
    }

    if (UAC.COMPUTE_SLOD && !limitedContext && !bestGuessIsRef) {
      // final boolean DEBUG_SLOD = false;

      // the overall lod
      // double overallLog10PofNull = AFresult.log10AlleleFrequencyPosteriors[0];
      double overallLog10PofF = AFresult.getLog10LikelihoodOfAFGT0();
      // if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF);

      List<Allele> allAllelesToUse = builder.make().getAlleles();

      // the forward lod
      VariantContext vcForward =
          calculateLikelihoods(
              tracker,
              refContext,
              stratifiedContexts,
              AlignmentContextUtils.ReadOrientation.FORWARD,
              allAllelesToUse,
              false,
              model,
              perReadAlleleLikelihoodMap);
      AFresult = afcm.get().getLog10PNonRef(vcForward, getAlleleFrequencyPriors(model));
      // double[] normalizedLog10Posteriors =
      // MathUtils.normalizeFromLog10(AFresult.log10AlleleFrequencyPosteriors, true);
      double forwardLog10PofNull = AFresult.getLog10LikelihoodOfAFEq0();
      double forwardLog10PofF = AFresult.getLog10LikelihoodOfAFGT0();
      // if ( DEBUG_SLOD ) System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ",
      // forwardLog10PofF=" + forwardLog10PofF);

      // the reverse lod
      VariantContext vcReverse =
          calculateLikelihoods(
              tracker,
              refContext,
              stratifiedContexts,
              AlignmentContextUtils.ReadOrientation.REVERSE,
              allAllelesToUse,
              false,
              model,
              perReadAlleleLikelihoodMap);
      AFresult = afcm.get().getLog10PNonRef(vcReverse, getAlleleFrequencyPriors(model));
      // normalizedLog10Posteriors =
      // MathUtils.normalizeFromLog10(AFresult.log10AlleleFrequencyPosteriors, true);
      double reverseLog10PofNull = AFresult.getLog10LikelihoodOfAFEq0();
      double reverseLog10PofF = AFresult.getLog10LikelihoodOfAFGT0();
      // if ( DEBUG_SLOD ) System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ",
      // reverseLog10PofF=" + reverseLog10PofF);

      double forwardLod = forwardLog10PofF + reverseLog10PofNull - overallLog10PofF;
      double reverseLod = reverseLog10PofF + forwardLog10PofNull - overallLog10PofF;
      // if ( DEBUG_SLOD ) System.out.println("forward lod=" + forwardLod + ", reverse lod=" +
      // reverseLod);

      // strand score is max bias between forward and reverse strands
      double strandScore = Math.max(forwardLod, reverseLod);
      // rescale by a factor of 10
      strandScore *= 10.0;
      // logger.debug(String.format("SLOD=%f", strandScore));

      if (!Double.isNaN(strandScore)) attributes.put("SB", strandScore);
    }

    // finish constructing the resulting VC
    builder.attributes(attributes);
    VariantContext vcCall = builder.make();

    // if we are subsetting alleles (either because there were too many or because some were not
    // polymorphic)
    // then we may need to trim the alleles (because the original VariantContext may have had to pad
    // at the end).
    if (myAlleles.size() != vc.getAlleles().size()
        && !limitedContext) // limitedContext callers need to handle allele trimming on their own to
                            // keep their perReadAlleleLikelihoodMap alleles in sync
    vcCall = VariantContextUtils.reverseTrimAlleles(vcCall);

    if (annotationEngine != null
        && !limitedContext) { // limitedContext callers need to handle annotations on their own by
                              // calling their own annotationEngine
      // Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
      final ReadBackedPileup pileup = rawContext.getBasePileup();
      stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);

      vcCall =
          annotationEngine.annotateContext(
              tracker, refContext, stratifiedContexts, vcCall, perReadAlleleLikelihoodMap);
    }

    return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PoFGT0));
  }