Java Code Examples for htsjdk.variant.variantcontext.VariantContext#hasGenotypes()
The following examples show how to use
htsjdk.variant.variantcontext.VariantContext#hasGenotypes() .
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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: SampleList.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.isMonomorphicInSamples() || !vc.hasGenotypes() ) {
return Collections.emptyMap();
}
final StringBuilder samples = new StringBuilder();
for ( final Genotype genotype : vc.getGenotypesOrderedByName() ) {
if ( genotype.isCalled() && !genotype.isHomRef() ){
if ( samples.length() > 0 ) {
samples.append(",");
}
samples.append(genotype.getSampleName());
}
}
if ( samples.length() == 0 ) {
return Collections.emptyMap();
}
return Collections.singletonMap(getKeyNames().get(0), samples.toString());
}
Example 3
| Source File: ValidationReport.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
@Override
public void update2(VariantContext eval, VariantContext comp, final ReferenceContext referenceContext, final ReadsContext readsContext, final FeatureContext featureContext) {
if ( comp != null ) { // we only need to consider sites in comp
if ( REQUIRE_IDENTICAL_ALLELES && (eval != null && haveDifferentAltAlleles(eval, comp)))
nDifferentAlleleSites++;
else {
SiteStatus evalStatus = calcSiteStatus(eval);
final Set<String> evalSamples = getWalker().getSampleNamesForEvaluation();
if ( comp.hasGenotypes() && ! evalSamples.isEmpty() && comp.hasGenotypes(evalSamples) )
// if we have genotypes in both eval and comp, subset comp down just the samples in eval
comp = comp.subContextFromSamples(evalSamples, false);
SiteStatus compStatus = calcSiteStatus(comp);
counts[compStatus.ordinal()][evalStatus.ordinal()]++;
}
}
}
Example 4
| Source File: ValidationReport.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
private SiteStatus calcSiteStatus(VariantContext vc) {
if ( vc == null ) return SiteStatus.NO_CALL;
if ( vc.isFiltered() ) return SiteStatus.FILTERED;
if ( vc.isMonomorphicInSamples() ) return SiteStatus.MONO;
if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphicInSamples was false and there are genotypes
if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
int ac = 0;
if ( vc.getNAlleles() > 2 ) {
return SiteStatus.POLY;
}
else
ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO;
} else {
return TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED ? SiteStatus.POLY : SiteStatus.NO_CALL; // we can't figure out what to do
}
}
Example 5
| Source File: RMSMappingQuality.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
/**
*
* @return the number of reads at the given site, calculated as InfoField {@link VCFConstants#DEPTH_KEY} minus the
* format field {@link GATKVCFConstants#MIN_DP_FORMAT_KEY} or DP of each of the HomRef genotypes at that site
* @throws UserException.BadInput if the {@link VCFConstants#DEPTH_KEY} is missing or if the calculated depth is <= 0
*/
@VisibleForTesting
private static int getNumOfReads(final VariantContext vc) {
if(vc.hasAttribute(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED)) {
int mqDP = vc.getAttributeAsInt(GATKVCFConstants.MAPPING_QUALITY_DEPTH_DEPRECATED, 0);
if (mqDP > 0) {
return mqDP;
}
}
//don't use the full depth because we don't calculate MQ for reference blocks
//don't count spanning deletion calls towards number of reads
int numOfReads = vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1);
if(vc.hasGenotypes()) {
for(final Genotype gt : vc.getGenotypes()) {
if(hasReferenceDepth(gt)) {
//site-level DP contribution will come from MIN_DP for gVCF-called reference variants or DP for BP resolution
if (gt.hasExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY)) {
numOfReads -= Integer.parseInt(gt.getExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY).toString());
} else if (gt.hasDP()) {
numOfReads -= gt.getDP();
}
}
else if(hasSpanningDeletionAllele(gt)) {
//site-level DP contribution will come from MIN_DP for gVCF-called reference variants or DP for BP resolution
if (gt.hasExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY)) {
numOfReads -= Integer.parseInt(gt.getExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY).toString());
} else if (gt.hasDP()) {
numOfReads -= gt.getDP();
}
}
}
}
if (numOfReads <= 0){
numOfReads = -1; //return -1 to result in a NaN
}
return numOfReads;
}
Example 6
| Source File: ChromosomeCounts.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
@Override
public Map<String, Object> annotate(final ReferenceContext ref,
final VariantContext vc,
AlleleLikelihoods<GATKRead, Allele> likelihoods) {
Utils.nonNull(vc);
if ( ! vc.hasGenotypes() ) {
return Collections.emptyMap();
}
return VariantContextUtils.calculateChromosomeCounts(vc, new LinkedHashMap<>(), true, Collections.emptySet());
}
Example 7
| Source File: GenotypeSummaries.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
@Override
public Map<String, Object> annotate(final ReferenceContext ref,
final VariantContext vc,
final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
Utils.nonNull(vc);
if ( ! vc.hasGenotypes() ) {
return Collections.emptyMap();
}
final Map<String,Object> returnMap = new LinkedHashMap<>();
returnMap.put(GATKVCFConstants.NOCALL_CHROM_KEY, vc.getNoCallCount());
final DescriptiveStatistics stats = new DescriptiveStatistics();
for( final Genotype g : vc.getGenotypes() ) {
if( g.hasGQ() ) {
stats.addValue(g.getGQ());
}
}
if( stats.getN() > 0L ) {
returnMap.put(GATKVCFConstants.GQ_MEAN_KEY, String.format("%.2f", stats.getMean()));
if( stats.getN() > 1L ) {
returnMap.put(GATKVCFConstants.GQ_STDEV_KEY, String.format("%.2f", stats.getStandardDeviation()));
}
}
return returnMap;
}
Example 8
| Source File: VariantAFEvaluator.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public void update1(VariantContext vc, final ReferenceContext referenceContext, final ReadsContext readsContext, final FeatureContext featureContext) {
vc.getStart();
if (vc == null || !vc.isSNP() || (getWalker().ignoreAC0Sites() && vc.isMonomorphicInSamples())) {
return;
}
for (final Genotype genotype : vc.getGenotypes()) {
// eval array
if (!genotype.isNoCall()) {
if (genotype.getPloidy() != PLOIDY) {
throw new UserException.BadInput("This tool only works with ploidy 2");
}
// add AF at this site
this.totalCalledSites += 1;
int numReferenceAlleles= genotype.countAllele(vc.getReference());
double varAFHere = (PLOIDY - numReferenceAlleles)/PLOIDY;
this.sumVariantAFs += varAFHere;
totalHetSites += numReferenceAlleles == 1 ? 1 : 0;
totalHomVarSites += numReferenceAlleles == 0 ? 1 : 0;
totalHomRefSites += numReferenceAlleles == 2 ? 1 : 0;
}
}
if (!vc.hasGenotypes()) {
// comp ( sites only thousand genomes )
this.totalCalledSites += 1;
this.sumVariantAFs += vc.getAttributeAsDouble("AF", 0.0);
}
}
Example 9
| Source File: VariantContextTestUtils.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public static void assertVariantContextsHaveSameGenotypes(final VariantContext actual, final VariantContext expected, final List<String> attributesToIgnore) {
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes");
if ( expected.hasGenotypes() ) {
BaseTest.assertEqualsSet(actual.getSampleNames(), expected.getSampleNames(), "sample names set");
Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names");
final Set<String> samples = expected.getSampleNames();
for ( final String sample : samples ) {
assertGenotypesAreEqual(actual.getGenotype(sample), expected.getGenotype(sample), attributesToIgnore);
}
}
}
Example 10
| 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 11
| Source File: RMSMappingQuality.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
/**
*
* @return the number of reads at the given site, trying first {@Link GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY},
* falling back to calculating the value as InfoField {@link VCFConstants#DEPTH_KEY} minus the
* format field {@link GATKVCFConstants#MIN_DP_FORMAT_KEY} or DP of each of the HomRef genotypes at that site.
* If neither of those is possible, will fall back to calculating the reads from the likelihoods data if provided.
* @throws UserException.BadInput if the {@link VCFConstants#DEPTH_KEY} is missing or if the calculated depth is <= 0
*/
@VisibleForTesting
static long getNumOfReads(final VariantContext vc,
final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
if(vc.hasAttribute(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY)) {
List<Long> mqTuple = VariantContextGetters.getAttributeAsLongList(vc, GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY,0L);
if (mqTuple.get(TOTAL_DEPTH_INDEX) > 0) {
return mqTuple.get(TOTAL_DEPTH_INDEX);
}
}
long numOfReads = 0;
if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) {
numOfReads = VariantContextGetters.getAttributeAsLong(vc, VCFConstants.DEPTH_KEY, -1L);
if(vc.hasGenotypes()) {
for(final Genotype gt : vc.getGenotypes()) {
if(gt.isHomRef()) {
//site-level DP contribution will come from MIN_DP for gVCF-called reference variants or DP for BP resolution
if (gt.hasExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY)) {
numOfReads -= Long.parseLong(gt.getExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY).toString());
} else if (gt.hasDP()) {
numOfReads -= gt.getDP();
}
}
}
}
// If there is no depth key, try to compute from the likelihoods
} else if (likelihoods != null && likelihoods.numberOfAlleles() != 0) {
for (int i = 0; i < likelihoods.numberOfSamples(); i++) {
for (GATKRead read : likelihoods.sampleEvidence(i)) {
if (read.getMappingQuality() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE) {
numOfReads++;
}
}
}
}
if (numOfReads <= 0) {
numOfReads = -1; //return -1 to result in a NaN
}
return numOfReads;
}
Example 12
| Source File: MendelianViolationEvaluator.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
public void update1(VariantContext vc, final ReferenceContext referenceContext, final ReadsContext readsContext, final FeatureContext featureContext) {
if (vc.isBiallelic() && vc.hasGenotypes()) { // todo -- currently limited to biallelic loci
if (mv.countFamilyViolations(sampleDB, null, vc) > 0){
nLociViolations++;
nViolations += mv.getViolationsCount();
mvRefRef_Var += mv.getParentsRefRefChildVar();
mvRefRef_Het += mv.getParentsRefRefChildHet();
mvRefHet_Var += mv.getParentsRefHetChildVar();
mvRefVar_Var += mv.getParentsRefVarChildVar();
mvRefVar_Ref += mv.getParentsRefVarChildRef();
mvVarHet_Ref += mv.getParentsVarHetChildRef();
mvVarVar_Ref += mv.getParentsVarVarChildRef();
mvVarVar_Het += mv.getParentsVarVarChildHet();
}
HomRefHomRef_HomRef += mv.getRefRefRef();
HetHet_Het += mv.getHetHetHet();
HetHet_HomRef += mv.getHetHetHomRef();
HetHet_HomVar += mv.getHetHetHomVar();
HomVarHomVar_HomVar += mv.getVarVarVar();
HomRefHomVAR_Het += mv.getRefVarHet();
HetHet_inheritedRef += mv.getParentsHetHetInheritedRef();
HetHet_inheritedVar += mv.getParentsHetHetInheritedVar();
HomRefHet_inheritedRef += mv.getParentsRefHetInheritedRef();
HomRefHet_inheritedVar += mv.getParentsRefHetInheritedVar();
HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef();
HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar();
if(mv.getFamilyCalledCount()>0 || mv.getFamilyLowQualsCount()>0 || mv.getFamilyCalledCount()>0){
nVariants++;
nFamCalled += mv.getFamilyCalledCount();
nLowQual += mv.getFamilyLowQualsCount();
nNoCall += mv.getFamilyNoCallCount();
nVarFamCalled += mv.getVarFamilyCalledCount();
}
else{
nSkipped++;
}
}
}
