public void setRead(final GATKRead read) {
if (!read.isEmpty()) {
this.read = read;
if (!read.isUnmapped())
loc =
genomeLocParser.createGenomeLoc(
read.getContig(), ReadUtils.getSoftStart(read), ReadUtils.getSoftEnd(read));
}
}
/**
* Add a read to the manager
*
* @param read the read to add
*/
public void addRead(final GATKRead read) {
if (read == null)
throw new IllegalArgumentException("read added to manager is null, which is not allowed");
// if the new read is on a different contig or we have too many reads, then we need to flush the
// queue and clear the map
final boolean tooManyReads = getNReadsInQueue() >= MAX_RECORDS_IN_MEMORY;
final boolean encounteredNewContig =
getNReadsInQueue() > 0 && !waitingReads.peek().read.getContig().equals(read.getContig());
if (tooManyReads || encounteredNewContig) {
if (DEBUG)
logger.warn(
"Flushing queue on "
+ (tooManyReads
? "too many reads"
: ("move to new contig: "
+ read.getContig()
+ " from "
+ waitingReads.peek().read.getContig()))
+ " at "
+ read.getStart());
final int targetQueueSize = encounteredNewContig ? 0 : MAX_RECORDS_IN_MEMORY / 2;
// write the required number of waiting reads to disk
while (getNReadsInQueue() > targetQueueSize) writer.addRead(waitingReads.poll().read);
}
final SplitRead splitRead = new SplitRead(read);
// fix overhangs, as needed
for (final Splice splice : splices) fixSplit(splitRead, splice);
// add the new read to the queue
waitingReads.add(splitRead);
}