/**
* Copy constructor
*
* @param other the VariantContext to copy
*/
protected VariantContext(VariantContext other) {
this(
other.getSource(),
other.getID(),
other.getChr(),
other.getStart(),
other.getEnd(),
other.getAlleles(),
other.getGenotypes(),
other.getLog10PError(),
other.getFiltersMaybeNull(),
other.getAttributes(),
other.REFERENCE_BASE_FOR_INDEL,
NO_VALIDATION);
}
private VariantCallContext generateEmptyContext(
RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, AlignmentContext> stratifiedContexts,
AlignmentContext rawContext) {
VariantContext vc;
if (UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
VariantContext vcInput =
UnifiedGenotyperEngine.getVCFromAllelesRod(
tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if (vcInput == null) return null;
vc =
new VariantContextBuilder(
"UG_call",
ref.getLocus().getContig(),
vcInput.getStart(),
vcInput.getEnd(),
vcInput.getAlleles())
.make();
} else {
// deal with bad/non-standard reference bases
if (!Allele.acceptableAlleleBases(new byte[] {ref.getBase()})) return null;
Set<Allele> alleles = new HashSet<Allele>();
alleles.add(Allele.create(ref.getBase(), true));
vc =
new VariantContextBuilder(
"UG_call",
ref.getLocus().getContig(),
ref.getLocus().getStart(),
ref.getLocus().getStart(),
alleles)
.make();
}
if (annotationEngine != null) {
// Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
final ReadBackedPileup pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
vc = annotationEngine.annotateContext(tracker, ref, stratifiedContexts, vc);
}
return new VariantCallContext(vc, false);
}
public static VariantContext createVariantContextWithPaddedAlleles(
VariantContext inputVC, boolean refBaseShouldBeAppliedToEndOfAlleles) {
// see if we need to pad common reference base from all alleles
boolean padVC;
// We need to pad a VC with a common base if the length of the reference allele is less than the
// length of the VariantContext.
// This happens because the position of e.g. an indel is always one before the actual event (as
// per VCF convention).
long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
if (inputVC.hasSymbolicAlleles()) padVC = true;
else if (inputVC.getReference().length() == locLength) padVC = false;
else if (inputVC.getReference().length() == locLength - 1) padVC = true;
else
throw new IllegalArgumentException(
"Badly formed variant context at location "
+ String.valueOf(inputVC.getStart())
+ " in contig "
+ inputVC.getChr()
+ ". Reference length must be at most one base shorter than location size");
// nothing to do if we don't need to pad bases
if (padVC) {
if (!inputVC.hasReferenceBaseForIndel())
throw new ReviewedStingException(
"Badly formed variant context at location "
+ inputVC.getChr()
+ ":"
+ inputVC.getStart()
+ "; no padded reference base is available.");
Byte refByte = inputVC.getReferenceBaseForIndel();
List<Allele> alleles = new ArrayList<Allele>();
for (Allele a : inputVC.getAlleles()) {
// get bases for current allele and create a new one with trimmed bases
if (a.isSymbolic()) {
alleles.add(a);
} else {
String newBases;
if (refBaseShouldBeAppliedToEndOfAlleles)
newBases = a.getBaseString() + new String(new byte[] {refByte});
else newBases = new String(new byte[] {refByte}) + a.getBaseString();
alleles.add(Allele.create(newBases, a.isReference()));
}
}
// now we can recreate new genotypes with trimmed alleles
GenotypesContext genotypes = GenotypesContext.create(inputVC.getNSamples());
for (final Genotype g : inputVC.getGenotypes()) {
List<Allele> inAlleles = g.getAlleles();
List<Allele> newGenotypeAlleles = new ArrayList<Allele>(g.getAlleles().size());
for (Allele a : inAlleles) {
if (a.isCalled()) {
if (a.isSymbolic()) {
newGenotypeAlleles.add(a);
} else {
String newBases;
if (refBaseShouldBeAppliedToEndOfAlleles)
newBases = a.getBaseString() + new String(new byte[] {refByte});
else newBases = new String(new byte[] {refByte}) + a.getBaseString();
newGenotypeAlleles.add(Allele.create(newBases, a.isReference()));
}
} else {
// add no-call allele
newGenotypeAlleles.add(Allele.NO_CALL);
}
}
genotypes.add(
new Genotype(
g.getSampleName(),
newGenotypeAlleles,
g.getLog10PError(),
g.getFilters(),
g.getAttributes(),
g.isPhased()));
}
return new VariantContextBuilder(inputVC).alleles(alleles).genotypes(genotypes).make();
} else return inputVC;
}
/**
* create a genome location, given a variant context
*
* @param genomeLocParser parser
* @param vc the variant context
* @return the genomeLoc
*/
public static final GenomeLoc getLocation(GenomeLocParser genomeLocParser, VariantContext vc) {
return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true);
}
static VariantContext reallyMergeIntoMNP(
VariantContext vc1, VariantContext vc2, ReferenceSequenceFile referenceFile) {
int startInter = vc1.getEnd() + 1;
int endInter = vc2.getStart() - 1;
byte[] intermediateBases = null;
if (startInter <= endInter) {
intermediateBases =
referenceFile.getSubsequenceAt(vc1.getChr(), startInter, endInter).getBases();
StringUtil.toUpperCase(intermediateBases);
}
MergedAllelesData mergeData =
new MergedAllelesData(
intermediateBases, vc1, vc2); // ensures that the reference allele is added
GenotypesContext mergedGenotypes = GenotypesContext.create();
for (final Genotype gt1 : vc1.getGenotypes()) {
Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
List<Allele> site1Alleles = gt1.getAlleles();
List<Allele> site2Alleles = gt2.getAlleles();
List<Allele> mergedAllelesForSample = new LinkedList<Allele>();
/* NOTE: Since merged alleles are added to mergedAllelesForSample in the SAME order as in the input VC records,
we preserve phase information (if any) relative to whatever precedes vc1:
*/
Iterator<Allele> all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next(); // this is OK, since allSamplesAreMergeable()
Allele mergedAllele = mergeData.ensureMergedAllele(all1, all2);
mergedAllelesForSample.add(mergedAllele);
}
double mergedGQ = Math.max(gt1.getLog10PError(), gt2.getLog10PError());
Set<String> mergedGtFilters =
new HashSet<
String>(); // Since gt1 and gt2 were unfiltered, the Genotype remains unfiltered
Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
if (phaseQual.PQ != null) mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);
Genotype mergedGt =
new Genotype(
gt1.getSampleName(),
mergedAllelesForSample,
mergedGQ,
mergedGtFilters,
mergedGtAttribs,
phaseQual.isPhased);
mergedGenotypes.add(mergedGt);
}
String mergedName = mergeVariantContextNames(vc1.getSource(), vc2.getSource());
double mergedLog10PError = Math.min(vc1.getLog10PError(), vc2.getLog10PError());
Set<String> mergedFilters =
new HashSet<
String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
Map<String, Object> mergedAttribs = mergeVariantContextAttributes(vc1, vc2);
// ids
List<String> mergedIDs = new ArrayList<String>();
if (vc1.hasID()) mergedIDs.add(vc1.getID());
if (vc2.hasID()) mergedIDs.add(vc2.getID());
String mergedID =
mergedIDs.isEmpty()
? VCFConstants.EMPTY_ID_FIELD
: Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
VariantContextBuilder mergedBuilder =
new VariantContextBuilder(
mergedName,
vc1.getChr(),
vc1.getStart(),
vc2.getEnd(),
mergeData.getAllMergedAlleles())
.id(mergedID)
.genotypes(mergedGenotypes)
.log10PError(mergedLog10PError)
.filters(mergedFilters)
.attributes(mergedAttribs);
VariantContextUtils.calculateChromosomeCounts(mergedBuilder, true);
return mergedBuilder.make();
}