@Override
public Map<String, Object> annotate(
final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
// Can only call from UnifiedGenotyper
if (!(walker instanceof UnifiedGenotyper)) {
if (!walkerIdentityCheckWarningLogged) {
if (walker != null)
logger.warn(
"Annotation will not be calculated, must be called from UnifiedGenotyper, not "
+ walker.getClass().getName());
else logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
walkerIdentityCheckWarningLogged = true;
}
return null;
}
if (stratifiedContexts.isEmpty()) return null;
// not meaningful when we're at an indel location: deletions that start at location N are by
// definition called at the position N-1, and at position N-1
// there are no informative deletions in the pileup
if (!vc.isSNP()) return null;
int deletions = 0;
int depth = 0;
for (Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet()) {
for (final PileupElement p : sample.getValue().getBasePileup()) {
depth++;
if (p.isDeletion()) deletions++;
}
}
Map<String, Object> map = new HashMap<>();
map.put(
getKeyNames().get(0),
String.format("%.2f", depth == 0 ? 0.0 : (double) deletions / (double) depth));
return map;
}
public CountedData map(
RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
final CountedData counter = new CountedData();
// For some reason RodWalkers get map calls with null trackers
if (tracker == null) return counter;
VariantContext vcComp = tracker.getFirstValue(alleles);
if (vcComp == null) return counter;
// todo - not sure I want this, may be misleading to filter extended indel events.
if (isInsideExtendedIndel(vcComp, ref)) return counter;
// Do not operate on variants that are not covered to the optional minimum depth
if (!context.hasReads()
|| (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
counter.nUncovered = 1L;
final GVstatus status = getGVstatus(vcComp);
if (status == GVstatus.T) counter.nAltNotCalled = 1L;
else if (status == GVstatus.F) counter.nRefNotCalled = 1L;
else counter.nNoStatusNotCalled = 1L;
return counter;
}
VariantCallContext call;
if (vcComp.isSNP()) {
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
} else if (vcComp.isIndel()) {
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
} else if (bamIsTruth) {
// assume it's a SNP if no variation is present; this is necessary so that we can test
// supposed monomorphic sites against the truth bam
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
} else {
logger.info(
"Not SNP or INDEL "
+ vcComp.getChr()
+ ":"
+ vcComp.getStart()
+ " "
+ vcComp.getAlleles());
return counter;
}
boolean writeVariant = true;
if (bamIsTruth) {
if (call.confidentlyCalled) {
// If truth is a confident REF call
if (call.isVariant()) {
if (vcComp.isVariant()) counter.nAltCalledAlt = 1L;
else {
counter.nAltCalledRef = 1L;
if (printInterestingSites)
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
}
}
// If truth is a confident ALT call
else {
if (vcComp.isVariant()) {
counter.nRefCalledAlt = 1L;
if (printInterestingSites)
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
} else counter.nRefCalledRef = 1L;
}
} else {
counter.nNotConfidentCalls = 1L;
if (printInterestingSites)
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
writeVariant = false;
}
} else {
// if (!vcComp.hasExtendedAttribute("GV"))
// throw new UserException.BadInput("Variant has no GV annotation in the INFO
// field. " + vcComp.getChr() + ":" + vcComp.getStart());
final GVstatus status = getGVstatus(vcComp);
if (call.isCalledAlt(callConf)) {
if (status == GVstatus.T) counter.nAltCalledAlt = 1L;
else if (status == GVstatus.F) {
counter.nRefCalledAlt = 1L;
if (printInterestingSites)
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
} else counter.nNoStatusCalledAlt = 1L;
} else if (call.isCalledRef(callConf)) {
if (status == GVstatus.T) {
counter.nAltCalledRef = 1L;
if (printInterestingSites)
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
} else if (status == GVstatus.F) counter.nRefCalledRef = 1L;
else counter.nNoStatusCalledRef = 1L;
} else {
counter.nNotConfidentCalls = 1L;
if (status == GVstatus.T) counter.nAltNotCalled = 1L;
else if (status == GVstatus.F) counter.nRefNotCalled = 1L;
else counter.nNoStatusNotCalled = 1L;
if (printInterestingSites)
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
writeVariant = false;
}
}
if (vcfWriter != null && writeVariant) {
if (!vcComp.hasAttribute(GATKVCFConstants.GENOTYPE_AND_VALIDATE_STATUS_KEY)) {
vcfWriter.add(
new VariantContextBuilder(vcComp)
.attribute(
GATKVCFConstants.GENOTYPE_AND_VALIDATE_STATUS_KEY,
call.isCalledAlt(callConf) ? "ALT" : "REF")
.make());
} else vcfWriter.add(vcComp);
}
return counter;
}