private void outputMissingInterval(final IntervalStratification stats) {
   final GenomeLoc interval = stats.getInterval();
   final boolean missing[] = new boolean[interval.size()];
   Arrays.fill(missing, true);
   for (AbstractStratification sample : stats.getElements()) {
     if (hasMissingStatuses(sample)) {
       int pos = 0;
       for (AbstractStratification locus : sample.getElements()) {
         if (locus.callableStatuses().isEmpty()) {
           missing[pos] = false;
         }
         pos++;
       }
     }
   }
   int start = -1;
   boolean insideMissing = false;
   for (int i = 0; i < missing.length; i++) {
     if (missing[i] && !insideMissing) {
       start = interval.getStart() + i;
       insideMissing = true;
     } else if (!missing[i] && insideMissing) {
       final int stop = interval.getStart() + i - 1;
       outputMissingInterval(interval.getContig(), start, stop);
       insideMissing = false;
     }
   }
   if (insideMissing) {
     outputMissingInterval(interval.getContig(), start, interval.getStop());
   }
 }
Example #2
0
  /** Prepare the output file and the list of available features. */
  public void initialize() {

    if (LIST) {
      AnnotationHelpUtils.listAnnotations();
      System.exit(0);
    }

    // get the list of all sample names from the variant VCF input rod, if applicable
    final List<String> rodName = Arrays.asList(variantCollection.variants.getName());
    final Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);

    if (USE_ALL_ANNOTATIONS)
      engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
    else
      engine =
          new VariantAnnotatorEngine(
              annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
    engine.initializeExpressions(expressionsToUse);
    engine.setExpressionAlleleConcordance(expressionAlleleConcordance);

    // setup the header fields
    // note that if any of the definitions conflict with our new ones, then we want to overwrite the
    // old ones
    final Set<VCFHeaderLine> hInfo = new HashSet<>();
    hInfo.addAll(engine.getVCFAnnotationDescriptions());
    for (final VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), rodName)) {
      if (isUniqueHeaderLine(line, hInfo)) hInfo.add(line);
    }
    // for the expressions, pull the info header line from the header of the resource rod
    for (final VariantAnnotatorEngine.VAExpression expression : engine.getRequestedExpressions()) {
      // special case the ID field
      if (expression.fieldName.equals("ID")) {
        hInfo.add(
            new VCFInfoHeaderLine(
                expression.fullName,
                1,
                VCFHeaderLineType.String,
                "ID field transferred from external VCF resource"));
        continue;
      }
      VCFInfoHeaderLine targetHeaderLine = null;
      for (final VCFHeaderLine line :
          GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName()))) {
        if (line instanceof VCFInfoHeaderLine) {
          final VCFInfoHeaderLine infoline = (VCFInfoHeaderLine) line;
          if (infoline.getID().equals(expression.fieldName)) {
            targetHeaderLine = infoline;
            break;
          }
        }
      }

      if (targetHeaderLine != null) {
        if (targetHeaderLine.getCountType() == VCFHeaderLineCount.INTEGER)
          hInfo.add(
              new VCFInfoHeaderLine(
                  expression.fullName,
                  targetHeaderLine.getCount(),
                  targetHeaderLine.getType(),
                  targetHeaderLine.getDescription()));
        else
          hInfo.add(
              new VCFInfoHeaderLine(
                  expression.fullName,
                  targetHeaderLine.getCountType(),
                  targetHeaderLine.getType(),
                  targetHeaderLine.getDescription()));
      } else {
        hInfo.add(
            new VCFInfoHeaderLine(
                expression.fullName,
                VCFHeaderLineCount.UNBOUNDED,
                VCFHeaderLineType.String,
                "Value transferred from another external VCF resource"));
      }
    }

    engine.makeHeaderInfoMap(hInfo);
    engine.invokeAnnotationInitializationMethods(hInfo);

    VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
    vcfWriter.writeHeader(vcfHeader);
  }