private Collection<VariantContext> getVariantContexts(
RefMetaDataTracker tracker, ReferenceContext ref) {
List<Feature> features = tracker.getValues(variants, ref.getLocus());
List<VariantContext> VCs = new ArrayList<VariantContext>(features.size());
for (Feature record : features) {
if (VariantContextAdaptors.canBeConvertedToVariantContext(record)) {
// we need to special case the HapMap format because indels aren't handled correctly
if (record instanceof RawHapMapFeature) {
// is it an indel?
RawHapMapFeature hapmap = (RawHapMapFeature) record;
if (hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING)
|| hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING)) {
// get the dbsnp object corresponding to this record (needed to help us distinguish
// between insertions and deletions)
VariantContext dbsnpVC = getDbsnp(hapmap.getName());
if (dbsnpVC == null || dbsnpVC.isMixed()) continue;
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(
RawHapMapFeature.DELETION,
Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
alleleMap.put(
RawHapMapFeature.INSERTION,
Allele.create(
(char) ref.getBase() + ((RawHapMapFeature) record).getAlleles()[1],
!dbsnpVC.isSimpleInsertion()));
hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions
hapmap.updatePosition(dbsnpVC.getStart());
if (hapmap.getStart() < ref.getWindow().getStart()) {
logger.warn(
"Hapmap record at "
+ ref.getLocus()
+ " represents an indel too large to be converted; skipping...");
continue;
}
}
}
// ok, we might actually be able to turn this record in a variant context
VariantContext vc =
VariantContextAdaptors.toVariantContext(variants.getName(), record, ref);
if (vc != null) // sometimes the track has odd stuff in it that can't be converted
VCs.add(vc);
}
}
return VCs;
}
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);
}