Exemplo n.º 1
0
  @Override
  public Map<String, Object> annotate(
      final RefMetaDataTracker tracker,
      final AnnotatorCompatible walker,
      final ReferenceContext ref,
      final Map<String, AlignmentContext> stratifiedContexts,
      final VariantContext vc,
      final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
    // Can only call from UnifiedGenotyper
    if (!(walker instanceof UnifiedGenotyper)) {
      if (!walkerIdentityCheckWarningLogged) {
        if (walker != null)
          logger.warn(
              "Annotation will not be calculated, must be called from UnifiedGenotyper, not "
                  + walker.getClass().getName());
        else logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
        walkerIdentityCheckWarningLogged = true;
      }
      return null;
    }

    if (stratifiedContexts.isEmpty()) return null;

    // not meaningful when we're at an indel location: deletions that start at location N are by
    // definition called at the position  N-1, and at position N-1
    // there are no informative deletions in the pileup
    if (!vc.isSNP()) return null;

    int deletions = 0;
    int depth = 0;
    for (Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet()) {
      for (final PileupElement p : sample.getValue().getBasePileup()) {
        depth++;
        if (p.isDeletion()) deletions++;
      }
    }
    Map<String, Object> map = new HashMap<>();
    map.put(
        getKeyNames().get(0),
        String.format("%.2f", depth == 0 ? 0.0 : (double) deletions / (double) depth));
    return map;
  }
Exemplo n.º 2
0
  @Override
  public CallableBaseState map(
      RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
    CalledState state;

    if (BaseUtils.isNBase(ref.getBase())) {
      state = CalledState.REF_N;
    } else {
      // count up the depths of all and QC+ bases
      int rawDepth = 0, QCDepth = 0, lowMAPQDepth = 0;
      for (PileupElement e : context.getBasePileup()) {
        rawDepth++;

        if (e.getMappingQual() <= maxLowMAPQ) lowMAPQDepth++;

        if (e.getMappingQual() >= minMappingQuality
            && (e.getQual() >= minBaseQuality || e.isDeletion())) {
          QCDepth++;
        }
      }

      // System.out.printf("%s rawdepth = %d QCDepth = %d lowMAPQ = %d%n", context.getLocation(),
      // rawDepth, QCDepth, lowMAPQDepth);
      if (rawDepth == 0) {
        state = CalledState.NO_COVERAGE;
      } else if (rawDepth >= minDepthLowMAPQ
          && MathUtils.ratio(lowMAPQDepth, rawDepth) >= maxLowMAPQFraction) {
        state = CalledState.POOR_MAPPING_QUALITY;
      } else if (QCDepth < minDepth) {
        state = CalledState.LOW_COVERAGE;
      } else if (rawDepth >= maxDepth && maxDepth != -1) {
        state = CalledState.EXCESSIVE_COVERAGE;
      } else {
        state = CalledState.CALLABLE;
      }
    }

    return new CallableBaseState(getToolkit().getGenomeLocParser(), context.getLocation(), state);
  }
  public Event map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

    boolean hasIndel = false;
    boolean hasInsertion = false;
    boolean hasPointEvent = false;

    int furthestStopPos = -1;

    // look at the rods for indels or SNPs
    if (tracker != null) {
      for (VariantContext vc : tracker.getValues(known)) {
        switch (vc.getType()) {
          case INDEL:
            hasIndel = true;
            if (vc.isSimpleInsertion()) hasInsertion = true;
            break;
          case SNP:
            hasPointEvent = true;
            break;
          case MIXED:
            hasPointEvent = true;
            hasIndel = true;
            if (vc.isSimpleInsertion()) hasInsertion = true;
            break;
          default:
            break;
        }
        if (hasIndel) furthestStopPos = vc.getEnd();
      }
    }

    // look at the normal context to get deletions and positions with high entropy
    final ReadBackedPileup pileup = context.getBasePileup();

    int mismatchQualities = 0, totalQualities = 0;
    final byte refBase = ref.getBase();
    for (PileupElement p : pileup) {

      // check the ends of the reads to see how far they extend
      furthestStopPos = Math.max(furthestStopPos, p.getRead().getAlignmentEnd());

      // is it a deletion or insertion?
      if (p.isDeletion() || p.isBeforeInsertion()) {
        hasIndel = true;
        if (p.isBeforeInsertion()) hasInsertion = true;
      }

      // look for mismatches
      else if (lookForMismatchEntropy) {
        if (p.getBase() != refBase) mismatchQualities += p.getQual();
        totalQualities += p.getQual();
      }
    }

    // make sure we're supposed to look for high entropy
    if (lookForMismatchEntropy
        && pileup.getNumberOfElements() >= minReadsAtLocus
        && (double) mismatchQualities / (double) totalQualities >= mismatchThreshold)
      hasPointEvent = true;

    // return null if no event occurred
    if (!hasIndel && !hasPointEvent) return null;

    // return null if we didn't find any usable reads/rods associated with the event
    if (furthestStopPos == -1) return null;

    GenomeLoc eventLoc = context.getLocation();
    if (hasInsertion)
      eventLoc =
          getToolkit()
              .getGenomeLocParser()
              .createGenomeLoc(eventLoc.getContig(), eventLoc.getStart(), eventLoc.getStart() + 1);

    EVENT_TYPE eventType =
        (hasIndel
            ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT)
            : EVENT_TYPE.POINT_EVENT);

    return new Event(eventLoc, furthestStopPos, eventType);
  }