/**
* Helper function to add the read underneath a pileup element to the map
*
* @param p Pileup element
* @param a Corresponding allele
* @param likelihood Allele likelihood
*/
public void add(PileupElement p, Allele a, Double likelihood) {
if (p == null) throw new IllegalArgumentException("Pileup element cannot be null");
if (p.getRead() == null)
throw new IllegalArgumentException("Read underlying pileup element cannot be null");
if (a == null) throw new IllegalArgumentException("Allele for add() cannot be null");
add(p.getRead(), a, likelihood);
}
public Event map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
boolean hasIndel = false;
boolean hasInsertion = false;
boolean hasPointEvent = false;
int furthestStopPos = -1;
// look at the rods for indels or SNPs
if (tracker != null) {
for (VariantContext vc : tracker.getValues(known)) {
switch (vc.getType()) {
case INDEL:
hasIndel = true;
if (vc.isSimpleInsertion()) hasInsertion = true;
break;
case SNP:
hasPointEvent = true;
break;
case MIXED:
hasPointEvent = true;
hasIndel = true;
if (vc.isSimpleInsertion()) hasInsertion = true;
break;
default:
break;
}
if (hasIndel) furthestStopPos = vc.getEnd();
}
}
// look at the normal context to get deletions and positions with high entropy
final ReadBackedPileup pileup = context.getBasePileup();
int mismatchQualities = 0, totalQualities = 0;
final byte refBase = ref.getBase();
for (PileupElement p : pileup) {
// check the ends of the reads to see how far they extend
furthestStopPos = Math.max(furthestStopPos, p.getRead().getAlignmentEnd());
// is it a deletion or insertion?
if (p.isDeletion() || p.isBeforeInsertion()) {
hasIndel = true;
if (p.isBeforeInsertion()) hasInsertion = true;
}
// look for mismatches
else if (lookForMismatchEntropy) {
if (p.getBase() != refBase) mismatchQualities += p.getQual();
totalQualities += p.getQual();
}
}
// make sure we're supposed to look for high entropy
if (lookForMismatchEntropy
&& pileup.getNumberOfElements() >= minReadsAtLocus
&& (double) mismatchQualities / (double) totalQualities >= mismatchThreshold)
hasPointEvent = true;
// return null if no event occurred
if (!hasIndel && !hasPointEvent) return null;
// return null if we didn't find any usable reads/rods associated with the event
if (furthestStopPos == -1) return null;
GenomeLoc eventLoc = context.getLocation();
if (hasInsertion)
eventLoc =
getToolkit()
.getGenomeLocParser()
.createGenomeLoc(eventLoc.getContig(), eventLoc.getStart(), eventLoc.getStart() + 1);
EVENT_TYPE eventType =
(hasIndel
? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT)
: EVENT_TYPE.POINT_EVENT);
return new Event(eventLoc, furthestStopPos, eventType);
}
@Override
protected boolean isUsableBase(final PileupElement p) {
return super.isUsableBase(p) && p.getRead().getCigar() != null;
}
@Override
protected Double getElementForPileupElement(final PileupElement p) {
final int offset = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0);
return (double) AnnotationUtils.getFinalVariantReadPosition(p.getRead(), offset);
}
public Map<Allele, Double> getLikelihoodsAssociatedWithPileupElement(final PileupElement p) {
if (!likelihoodReadMap.containsKey(p.getRead())) return null;
return likelihoodReadMap.get(p.getRead());
}
/**
* Does the current map contain the key associated with a particular SAM record in pileup?
*
* @param p Pileup element
* @return true if the map contains pileup element, else false
*/
public boolean containsPileupElement(final PileupElement p) {
return likelihoodReadMap.containsKey(p.getRead());
}