/** 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();
}
}
/**
* 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();
}