private T processActiveRegion(
final ActiveRegion activeRegion,
final LinkedHashSet<GATKSAMRecord> reads,
final Queue<ActiveRegion> workQueue,
final T sum,
final ActiveRegionWalker<M, T> walker) {
final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
for (final GATKSAMRecord read : reads) {
final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc(read);
if (activeRegion.getLocation().overlapsP(readLoc)) {
// The region which the highest amount of overlap is chosen as the primary region for the
// read (tie breaking is done as right most region)
long maxOverlap = activeRegion.getLocation().sizeOfOverlap(readLoc);
ActiveRegion bestRegion = activeRegion;
for (final ActiveRegion otherRegionToTest : workQueue) {
if (otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap) {
maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap(readLoc);
bestRegion = otherRegionToTest;
}
}
bestRegion.add(read);
// The read is also added to all other regions in which it overlaps but marked as
// non-primary
if (walker.wantsNonPrimaryReads()) {
if (!bestRegion.equals(activeRegion)) {
activeRegion.add(read);
}
for (final ActiveRegion otherRegionToTest : workQueue) {
if (!bestRegion.equals(otherRegionToTest)
&& otherRegionToTest.getExtendedLoc().overlapsP(readLoc)) {
otherRegionToTest.add(read);
}
}
}
placedReads.add(read);
} else if (activeRegion.getExtendedLoc().overlapsP(readLoc)
&& walker.wantsNonPrimaryReads()) {
activeRegion.add(read);
}
}
reads.removeAll(
placedReads); // remove all the reads which have been placed into their active region
// WARNING: This hashset relies on reads being exactly equal when they are placed in the list as
// when they are removed. So the ActiveRegionWalker can't modify the reads in any way.
logger.debug(
">> Map call with "
+ activeRegion.getReads().size()
+ " "
+ (activeRegion.isActive ? "active" : "inactive")
+ " reads @ "
+ activeRegion.getLocation()
+ " with full extent: "
+ activeRegion.getReferenceLoc());
final M x = walker.map(activeRegion, null);
return walker.reduce(x, sum);
}
