/**
   * Returns a context identical to this with the REF and ALT alleles reverse complemented.
   *
   * @param vc variant context
   * @return new vc
   */
  public static VariantContext reverseComplement(VariantContext vc) {
    // create a mapping from original allele to reverse complemented allele
    HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size());
    for (Allele originalAllele : vc.getAlleles()) {
      Allele newAllele;
      if (originalAllele.isNoCall() || originalAllele.isNull()) newAllele = originalAllele;
      else
        newAllele =
            Allele.create(
                BaseUtils.simpleReverseComplement(originalAllele.getBases()),
                originalAllele.isReference());
      alleleMap.put(originalAllele, newAllele);
    }

    // create new Genotype objects
    GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
    for (final Genotype genotype : vc.getGenotypes()) {
      List<Allele> newAlleles = new ArrayList<Allele>();
      for (Allele allele : genotype.getAlleles()) {
        Allele newAllele = alleleMap.get(allele);
        if (newAllele == null) newAllele = Allele.NO_CALL;
        newAlleles.add(newAllele);
      }
      newGenotypes.add(Genotype.modifyAlleles(genotype, newAlleles));
    }

    return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make();
  }
Example #2
0
    private Allele ensureMergedAllele(
        Allele all1, Allele all2, boolean creatingReferenceForFirstTime) {
      AlleleOneAndTwo all12 = new AlleleOneAndTwo(all1, all2);
      Allele mergedAllele = mergedAlleles.get(all12);

      if (mergedAllele == null) {
        byte[] bases1 = all1.getBases();
        byte[] bases2 = all2.getBases();

        byte[] mergedBases = new byte[bases1.length + intermediateLength + bases2.length];
        System.arraycopy(bases1, 0, mergedBases, 0, bases1.length);
        if (intermediateBases != null)
          System.arraycopy(intermediateBases, 0, mergedBases, bases1.length, intermediateLength);
        System.arraycopy(bases2, 0, mergedBases, bases1.length + intermediateLength, bases2.length);

        mergedAllele = Allele.create(mergedBases, creatingReferenceForFirstTime);
        mergedAlleles.put(all12, mergedAllele);
      }

      return mergedAllele;
    }
  private static AlleleMapper resolveIncompatibleAlleles(
      Allele refAllele, VariantContext vc, Set<Allele> allAlleles) {
    if (refAllele.equals(vc.getReference())) return new AlleleMapper(vc);
    else {
      // we really need to do some work.  The refAllele is the longest reference allele seen at this
      // start site.  So imagine it is:
      //
      // refAllele: ACGTGA
      // myRef:     ACGT
      // myAlt:     -
      //
      // We need to remap all of the alleles in vc to include the extra GA so that
      // myRef => refAllele and myAlt => GA
      //

      Allele myRef = vc.getReference();
      if (refAllele.length() <= myRef.length())
        throw new ReviewedStingException(
            "BUG: myRef=" + myRef + " is longer than refAllele=" + refAllele);
      byte[] extraBases =
          Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length());

      //            System.out.printf("Remapping allele at %s%n", vc);
      //            System.out.printf("ref   %s%n", refAllele);
      //            System.out.printf("myref %s%n", myRef );
      //            System.out.printf("extrabases %s%n", new String(extraBases));

      Map<Allele, Allele> map = new HashMap<Allele, Allele>();
      for (Allele a : vc.getAlleles()) {
        if (a.isReference()) map.put(a, refAllele);
        else {
          Allele extended = Allele.extend(a, extraBases);
          for (Allele b : allAlleles) if (extended.equals(b)) extended = b;
          //                    System.out.printf("  Extending %s => %s%n", a, extended);
          map.put(a, extended);
        }
      }

      // debugging
      //            System.out.printf("mapping %s%n", map);

      return new AlleleMapper(map);
    }
  }
  public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) {
    // see if we need to trim common reference base from all alleles
    boolean trimVC;

    // We need to trim common reference base from all alleles in all genotypes if a ref base is
    // common to all alleles
    Allele refAllele = inputVC.getReference();
    if (!inputVC.isVariant()) trimVC = false;
    else if (refAllele.isNull()) trimVC = false;
    else {
      trimVC =
          (AbstractVCFCodec.computeForwardClipping(
                  new ArrayList<Allele>(inputVC.getAlternateAlleles()),
                  inputVC.getReference().getDisplayString())
              > 0);
    }

    // nothing to do if we don't need to trim bases
    if (trimVC) {
      List<Allele> alleles = new ArrayList<Allele>();
      GenotypesContext genotypes = GenotypesContext.create();

      // set the reference base for indels in the attributes
      Map<String, Object> attributes = new TreeMap<String, Object>(inputVC.getAttributes());

      Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();

      for (Allele a : inputVC.getAlleles()) {
        if (a.isSymbolic()) {
          alleles.add(a);
          originalToTrimmedAlleleMap.put(a, a);
        } else {
          // get bases for current allele and create a new one with trimmed bases
          byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length());
          Allele trimmedAllele = Allele.create(newBases, a.isReference());
          alleles.add(trimmedAllele);
          originalToTrimmedAlleleMap.put(a, trimmedAllele);
        }
      }

      // detect case where we're trimming bases but resulting vc doesn't have any null allele. In
      // that case, we keep original representation
      // example: mixed records such as {TA*,TGA,TG}
      boolean hasNullAlleles = false;

      for (Allele a : originalToTrimmedAlleleMap.values()) {
        if (a.isNull()) hasNullAlleles = true;
        if (a.isReference()) refAllele = a;
      }

      if (!hasNullAlleles) return inputVC;
      // now we can recreate new genotypes with trimmed alleles
      for (final Genotype genotype : inputVC.getGenotypes()) {

        List<Allele> originalAlleles = genotype.getAlleles();
        List<Allele> trimmedAlleles = new ArrayList<Allele>();
        for (Allele a : originalAlleles) {
          if (a.isCalled()) trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
          else trimmedAlleles.add(Allele.NO_CALL);
        }
        genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles));
      }

      final VariantContextBuilder builder = new VariantContextBuilder(inputVC);
      return builder
          .alleles(alleles)
          .genotypes(genotypes)
          .attributes(attributes)
          .referenceBaseForIndel(new Byte(inputVC.getReference().getBases()[0]))
          .make();
    }

    return inputVC;
  }
 public static boolean isTransversion(Allele ref, Allele alt) {
   return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0])
       == BaseUtils.BaseSubstitutionType.TRANSVERSION;
 }