Ejemplo n.º 1
0
 /** Clean up the list of splices */
 private void cleanSplices() {
   final int targetQueueSize = splices.size() / 2;
   final Iterator<Splice> iter = splices.iterator();
   for (int i = 0; i < targetQueueSize; i++) {
     iter.next();
     iter.remove();
   }
 }
Ejemplo n.º 2
0
  /**
   * Add a new observed split to the list to use
   *
   * @param contig the contig
   * @param start the start of the split, inclusive
   * @param end the end of the split, inclusive
   */
  public void addSplicePosition(final String contig, final int start, final int end) {
    if (doNotFixOverhangs) return;

    // is this a new splice?  if not, we are done
    final Splice splice = new Splice(contig, start, end);
    if (splices.contains(splice)) return;

    // initialize it with the reference context
    // we don't want to do this until we know for sure that it's a new splice position
    splice.initialize(referenceReader);

    // clear the set of old split positions seen if we hit a new contig
    final boolean sameContig =
        splices.isEmpty() || splices.iterator().next().loc.getContig().equals(contig);
    if (!sameContig) splices.clear();

    // run this position against the existing reads
    for (final SplitRead read : waitingReads) fixSplit(read, splice);

    splices.add(splice);

    if (splices.size() > MAX_SPLICES_TO_KEEP) cleanSplices();
  }