Exemplo n.º 1
0
  /**
   * Process all remaining intervals
   *
   * @param result number of loci processed by the walker
   */
  @Override
  public void onTraversalDone(final Long result) {
    for (GenomeLoc interval : intervalMap.keySet())
      outputStatsToVCF(intervalMap.get(interval), UNCOVERED_ALLELE);

    GenomeLoc interval = intervalListIterator.peek();
    while (interval != null) {
      outputStatsToVCF(createIntervalStatistic(interval), UNCOVERED_ALLELE);
      intervalListIterator.next();
      interval = intervalListIterator.peek();
    }

    if (thresholds.missingTargets != null) {
      thresholds.missingTargets.close();
    }
  }
Exemplo n.º 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);
   }
 }