Java Code Examples for htsjdk.variant.variantcontext.VariantContext#isVariant()
The following examples show how to use
htsjdk.variant.variantcontext.VariantContext#isVariant() .
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Example 1
| Source File: StrandBiasTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
@Override
//template method for calculating strand bias annotations using the three different methods
public Map<String, Object> annotate(final ReferenceContext ref,
final VariantContext vc,
final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
Utils.nonNull(vc);
if ( !vc.isVariant() ) {
return Collections.emptyMap();
}
// if the genotype and strand bias are provided, calculate the annotation from the Genotype (GT) field
if ( vc.hasGenotypes() ) {
for (final Genotype g : vc.getGenotypes()) {
if (g.hasAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY)) {
return calculateAnnotationFromGTfield(vc.getGenotypes());
}
}
}
if (likelihoods != null) {
return calculateAnnotationFromLikelihoods(likelihoods, vc);
}
return Collections.emptyMap();
}
Example 2
| Source File: ExcessHet.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
@Override
public Map<String, Object> annotate(final ReferenceContext ref,
final VariantContext vc,
final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
GenotypesContext genotypes = getFounderGenotypes(vc);
if (genotypes == null || !vc.isVariant()) {
return Collections.emptyMap();
}
final Pair<Integer, Double> sampleCountEH = calculateEH(vc, genotypes);
final int sampleCount = sampleCountEH.getLeft();
final double eh = sampleCountEH.getRight();
if (sampleCount < 1) {
return Collections.emptyMap();
}
return Collections.singletonMap(getKeyNames().get(0), (Object) String.format("%.4f", eh));
}
Example 3
| Source File: MappingQualityZero.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
@Override
public Map<String, Object> annotate(final ReferenceContext ref,
final VariantContext vc,
final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
Utils.nonNull(vc);
if (!vc.isVariant() || likelihoods == null){
return Collections.emptyMap();
}
//NOTE: unlike other annotations, this one returns 0 if likelihoods are empty
final long mq0 = IntStream.range(0, likelihoods.numberOfSamples()).boxed()
.flatMap(s -> likelihoods.sampleEvidence(s).stream())
.filter(r -> r.getMappingQuality() == 0)
.count();
return Collections.singletonMap(getKeyNames().get(0), formattedValue(mq0));
}
Example 4
| Source File: InbreedingCoeff.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
@Override
public Map<String, Object> annotate(final ReferenceContext ref,
final VariantContext vc,
final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
Utils.nonNull(vc);
final GenotypesContext genotypes = getFounderGenotypes(vc);
if (genotypes == null || genotypes.size() < MIN_SAMPLES || !vc.isVariant()) {
logger.warn("InbreedingCoeff will not be calculated; at least " + MIN_SAMPLES + " samples must have called genotypes");
return Collections.emptyMap();
}
final Pair<Integer, Double> sampleCountCoeff = calculateIC(vc, genotypes);
final int sampleCount = sampleCountCoeff.getLeft();
final double F = sampleCountCoeff.getRight();
if (sampleCount < MIN_SAMPLES) {
logger.warn("InbreedingCoeff will not be calculated for at least one position; at least " + MIN_SAMPLES + " samples must have called genotypes");
return Collections.emptyMap();
}
return Collections.singletonMap(getKeyNames().get(0), String.format("%.4f", F));
}
Example 5
| Source File: SnpEffPositionModifier.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
@Override
public List<Object> getRelevantStates(
final ReferenceContext referenceContext,
final ReadsContext readsContext,
final FeatureContext featureContext,
final VariantContext comp,
final String compName,
final VariantContext eval,
final String evalName,
final String sampleName,
final String FamilyName)
{
final List<Object> relevantStates = new ArrayList<>();
if (eval != null && eval.isVariant() && eval.hasAttribute(EFFECT_KEY)) {
final SnpEffUtil.EffectType effectType = SnpEffUtil.EffectType.valueOf(
eval.getAttribute(EFFECT_KEY).toString());
if (SnpEffUtil.isSubTypeOf(effectType, SnpEffUtil.EffectType.EXON)) relevantStates.add(PositionModifier.GENE.name());
if (SnpEffUtil.isSubTypeOf(effectType, SnpEffUtil.EffectType.CDS)) relevantStates.add(PositionModifier.CODING_REGION.name());
if (SnpEffUtil.isSubTypeOf(effectType, SnpEffUtil.EffectType.STOP_GAINED)) relevantStates.add(PositionModifier.STOP_GAINED.name());
if (SnpEffUtil.isSubTypeOf(effectType, SnpEffUtil.EffectType.STOP_LOST)) relevantStates.add(PositionModifier.STOP_LOST.name());
if (SnpEffUtil.isSubTypeOf(effectType, SnpEffUtil.EffectType.SPLICE_SITE_ACCEPTOR) ||
SnpEffUtil.isSubTypeOf(effectType, SnpEffUtil.EffectType.SPLICE_SITE_DONOR))
relevantStates.add(PositionModifier.SPLICE_SITE.name());
}
return relevantStates;
}
Example 6
| Source File: AlleleCount.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public List<Object> getRelevantStates(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
if (eval != null) {
int AC = 0; // by default, the site is considered monomorphic
try {
if ( eval.isBiallelic() ) {
if ( eval.hasAttribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY) ) {
// the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1)
AC = Math.min(eval.getAttributeAsInt(GATKVCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom);
} else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
}
}
} catch ( ClassCastException e ) {
// protect ourselves from bad inputs
// TODO -- fully decode VC
}
if ( AC == 0 && eval.isVariant() ) {
// fall back to the direct calculation
for (Allele allele : eval.getAlternateAlleles())
AC = Math.max(AC, eval.getCalledChrCount(allele));
}
// make sure that the AC isn't invalid
if ( AC > nchrom )
throw new UserException(String.format("The AC value (%d) at position %s:%d " +
"is larger than the number of chromosomes over all samples (%d)", AC,
eval.getContig(), eval.getStart(), nchrom));
return Collections.singletonList((Object) AC);
} else {
return Collections.emptyList();
}
}
Example 7
| Source File: ReferenceConfidenceModelUnitTest.java From gatk-protected with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
private void checkReferenceModelResult(final RefConfData data, final List<VariantContext> contexts, final List<Integer> expectedDPs, final List<VariantContext> calls) {
Assert.assertNotNull(contexts);
final SimpleInterval loc = data.getActiveRegion().getExtendedSpan();
final List<Boolean> seenBP = new ArrayList<>(Collections.nCopies(data.getActiveRegion().getSpan().size(), false));
for ( int i = 0; i < loc.size(); i++ ) {
final GenomeLoc curPos = parser.createGenomeLoc(loc.getContig(), loc.getStart() + i);
final VariantContext call = model.getOverlappingVariantContext(curPos, calls);
final VariantContext refModel = model.getOverlappingVariantContext(curPos, contexts);
if ( ! data.getActiveRegion().getSpan().contains(curPos) ) {
// part of the extended interval, but not the full interval
Assert.assertNull(refModel);
continue;
}
if ( call != null ) {
if (call.isVariant() && refModel.getType() == VariantContext.Type.SYMBOLIC ) {
//Assert.assertEquals(refModel, call, "Should have found call " + call + " but found " + refModel + " instead");
Assert.assertTrue(call.getReference().length() > 1); // must be a deletion.
Assert.assertTrue(call.getStart() < refModel.getStart()); // the deletion must not start at the same position
Assert.assertEquals(call.getReference().getBaseString().substring(refModel.getStart() - call.getStart(),
refModel.getStart() - call.getStart() + 1), refModel.getReference().getBaseString(), "" + data.getRefHap()); // the reference must be the same.
Assert.assertTrue(refModel.getGenotype(0).getGQ() <= 0); // No confidence in the reference hom-ref call across the deletion
Assert.assertEquals(refModel.getAlleles().size(),2); // the reference and the lonelly <NON_REF>
Assert.assertEquals(refModel.getAlleles().get(1), GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
} else {
Assert.assertEquals(refModel, call, "Should have found call " + call + " but found " + refModel + " instead");
}
} else {
final int expectedDP = expectedDPs.get(curPos.getStart() - data.getActiveRegion().getSpan().getStart());
Assert.assertEquals(refModel.getStart(), loc.getStart() + i);
Assert.assertEquals(refModel.getEnd(), loc.getStart() + i);
Assert.assertFalse(refModel.hasLog10PError());
Assert.assertEquals(refModel.getAlternateAlleles().size(), 1);
Assert.assertEquals(refModel.getAlternateAllele(0), GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
Assert.assertTrue(refModel.hasGenotype(sample));
final Genotype g = refModel.getGenotype(sample);
Assert.assertTrue(g.hasAD());
Assert.assertTrue(g.hasDP());
Assert.assertEquals(g.getDP(), expectedDP);
Assert.assertTrue(g.hasGQ());
Assert.assertTrue(g.hasPL());
}
final VariantContext vc = call == null ? refModel : call;
if ( curPos.getStart() == vc.getStart() ) {
for ( int pos = vc.getStart(); pos <= vc.getEnd(); pos++ ) {
final int j = pos - data.getActiveRegion().getSpan().getStart();
Assert.assertFalse(seenBP.get(j));
seenBP.set(j, true);
}
}
}
for ( int i = 0; i < seenBP.size(); i++ ) {
Assert.assertEquals((boolean)seenBP.get(i), true);
}
}
Example 8
| Source File: CallingMetricAccumulator.java From picard with MIT License | 4 votes |
|
/** Returns true if the variant is --NOT-- interesting enough to be included in metrics calculations. */
static private boolean isVariantExcluded(final VariantContext vc) {
// If the entire record is not a variant, exclude it
return !vc.isVariant() || vc.getGenotypes().stream().allMatch(Genotype::isHomRef);
}
Example 9
| Source File: VariantDataManager.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
private boolean isValidVariant( final VariantContext evalVC, final VariantContext trainVC, final boolean TRUST_ALL_POLYMORPHIC) {
return trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && checkVariationClass( evalVC, trainVC ) &&
(TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphicInSamples());
}
Example 10
| Source File: Degeneracy.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
public List<Object> getRelevantStates(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("all");
if (eval != null && eval.isVariant()) {
String type = null;
String aa = null;
Integer frame = null;
if (eval.hasAttribute("refseq.functionalClass")) {
aa = eval.getAttributeAsString("refseq.variantAA", null);
frame = eval.getAttributeAsInt("refseq.frame", 0);
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtype = eval.getAttributeAsString(key, null);
if ( newtype != null &&
( type == null ||
( type.equals("silent") && !newtype.equals("silent") ) ||
( type.equals("missense") && newtype.equals("nonsense") ) )
) {
type = newtype;
String aakey = String.format("refseq.variantAA_%d", annotationId);
aa = eval.getAttributeAsString(aakey, null);
if (aa != null) {
String framekey = String.format("refseq.frame_%d", annotationId);
if (eval.hasAttribute(framekey)) {
frame = eval.getAttributeAsInt(framekey, 0);
}
}
}
annotationId++;
} while (eval.hasAttribute(key));
}
if (aa != null && degeneracies.containsKey(aa) && frame != null) {
relevantStates.add(degeneracies.get(aa).get(frame));
}
}
return relevantStates;
}
