예제 #1
0
  private void writeDifferences(
      final List<VariantContext> source1Alleles, final List<VariantContext> source2Alleles) {
    int currentIndex1 = 0, currentIndex2 = 0;
    final int size1 = source1Alleles.size(), size2 = source2Alleles.size();
    VariantContext current1 = source1Alleles.get(0);
    VariantContext current2 = source2Alleles.get(0);

    while (currentIndex1 < size1 || currentIndex2 < size2) {
      if (current1 == null) {
        writeOne(current2, source2, null);
        currentIndex2++;
        current2 = (currentIndex2 < size2 ? source2Alleles.get(currentIndex2) : null);
      } else if (current2 == null) {
        writeOne(current1, source1, null);
        currentIndex1++;
        current1 = (currentIndex1 < size1 ? source1Alleles.get(currentIndex1) : null);
      } else {

        final GenomeLoc loc1 = getToolkit().getGenomeLocParser().createGenomeLoc(current1);
        final GenomeLoc loc2 = getToolkit().getGenomeLocParser().createGenomeLoc(current2);

        if (loc1.getStart() == loc2.getStart() || loc1.overlapsP(loc2)) {
          String status;
          if (loc1.getStart() == loc2.getStart()) {
            final String allele1 = current1.getAlternateAllele(0).getBaseString();
            final String allele2 = current2.getAlternateAllele(0).getBaseString();
            if (allele1.indexOf(allele2) != -1 || allele2.indexOf(allele1) != -1)
              status = ONE_ALLELE_SUBSET_OF_OTHER_STATUS;
            else status = SAME_START_DIFFERENT_ALLELES_STATUS;
          } else {
            status = OVERLAPPING_EVENTS_STATUS;
          }

          writeOne(current1, INTERSECTION_SET, status);
          currentIndex1++;
          currentIndex2++;
          current1 = (currentIndex1 < size1 ? source1Alleles.get(currentIndex1) : null);
          current2 = (currentIndex2 < size2 ? source2Alleles.get(currentIndex2) : null);
        } else if (loc1.isBefore(loc2)) {
          writeOne(current1, source1, null);
          currentIndex1++;
          current1 = (currentIndex1 < size1 ? source1Alleles.get(currentIndex1) : null);
        } else {
          writeOne(current2, source2, null);
          currentIndex2++;
          current2 = (currentIndex2 < size2 ? source2Alleles.get(currentIndex2) : null);
        }
      }
    }
  }
예제 #2
0
 /**
  * Outputs all intervals that are behind the current reference locus
  *
  * @param refLocus the current reference locus
  * @param refBase the reference allele
  */
 private void outputFinishedIntervals(final GenomeLoc refLocus, final byte refBase) {
   // output any intervals that were finished
   final List<GenomeLoc> toRemove = new LinkedList<>();
   for (GenomeLoc key : intervalMap.keySet()) {
     if (key.isBefore(refLocus)) {
       final IntervalStratification intervalStats = intervalMap.get(key);
       outputStatsToVCF(intervalStats, Allele.create(refBase, true));
       if (hasMissingLoci(intervalStats)) {
         outputMissingInterval(intervalStats);
       }
       toRemove.add(key);
     }
   }
   for (GenomeLoc key : toRemove) {
     intervalMap.remove(key);
   }
 }
예제 #3
0
  private void writeAndPurgeAllEqualVariants(
      final List<VariantContext> sourceVCs1,
      final List<VariantContext> sourceVCs2,
      final String status) {

    int currentIndex1 = 0, currentIndex2 = 0;
    int size1 = sourceVCs1.size(), size2 = sourceVCs2.size();
    VariantContext current1 = (currentIndex1 < size1 ? sourceVCs1.get(currentIndex1) : null);
    VariantContext current2 = (currentIndex2 < size2 ? sourceVCs2.get(currentIndex2) : null);

    while (current1 != null && current2 != null) {

      final GenomeLoc loc1 = getToolkit().getGenomeLocParser().createGenomeLoc(current1);
      final GenomeLoc loc2 = getToolkit().getGenomeLocParser().createGenomeLoc(current2);

      if (loc1.equals(loc2)
          || (loc1.getStart() == loc2.getStart()
              && (current1.getAlternateAlleles().size() > 1
                  || current2.getAlternateAlleles().size() > 1))) {
        // test the alleles
        if (determineAndWriteOverlap(current1, current2, status)) {
          sourceVCs1.remove(currentIndex1);
          sourceVCs2.remove(currentIndex2);
          size1--;
          size2--;
        } else {
          currentIndex1++;
          currentIndex2++;
        }
        current1 = (currentIndex1 < size1 ? sourceVCs1.get(currentIndex1) : null);
        current2 = (currentIndex2 < size2 ? sourceVCs2.get(currentIndex2) : null);
      } else if (loc1.isBefore(loc2)) {
        currentIndex1++;
        current1 = (currentIndex1 < size1 ? sourceVCs1.get(currentIndex1) : null);
      } else {
        currentIndex2++;
        current2 = (currentIndex2 < size2 ? sourceVCs2.get(currentIndex2) : null);
      }
    }
  }