Java Code Examples for htsjdk.variant.variantcontext.VariantContext#isMonomorphicInSamples()
The following examples show how to use
htsjdk.variant.variantcontext.VariantContext#isMonomorphicInSamples() .
You can vote up the ones you like or vote down the ones you don't like,
and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
| 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 2
| 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 3
| Source File: VariantSummary.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public void update2(VariantContext eval, VariantContext comp, ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext) {
if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) )
return;
final Type type = getType(eval);
if ( type == null )
return;
TypeSampleMap titvTable = null;
// update DP, if possible
if ( eval.hasAttribute(VCFConstants.DEPTH_KEY) )
depthPerSample.inc(type, ALL);
// update counts
allVariantCounts.inc(type, ALL);
// type specific calculations
if ( type == Type.SNP && eval.isBiallelic() ) {
titvTable = GATKVariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample;
titvTable.inc(type, ALL);
}
// novelty calculation
if ( comp != null || (type == Type.CNV && overlapsKnownCNV(eval, featureContext)))
knownVariantCounts.inc(type, ALL);
// per sample metrics
for (final Genotype g : eval.getGenotypes()) {
if ( ! g.isNoCall() && ! g.isHomRef() ) {
countsPerSample.inc(type, g.getSampleName());
// update transition / transversion ratio
if ( titvTable != null ) titvTable.inc(type, g.getSampleName());
if ( g.hasDP() )
depthPerSample.inc(type, g.getSampleName());
}
}
}
Example 4
| 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 5
| Source File: MultiallelicSummary.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public void update2(VariantContext eval, VariantContext comp, final ReferenceContext referenceContext, final ReadsContext readsContext, final FeatureContext featureContext) {
if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) )
return;
// update counts
switch ( eval.getType() ) {
case SNP:
nSNPs++;
if ( !eval.isBiallelic() ) {
nMultiSNPs++;
calculatePairwiseTiTv(eval);
calculateSNPPairwiseNovelty(eval, comp);
}
break;
case INDEL:
nIndels++;
if ( !eval.isBiallelic() ) {
nMultiIndels++;
calculateIndelPairwiseNovelty(eval, comp);
}
break;
default:
//throw new UserException.BadInput("Unexpected variant context type: " + eval);
break;
}
return;
}
Example 6
| Source File: IndelLengthHistogram.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
@Override
public void update1(final VariantContext eval, final ReferenceContext referenceContext, final ReadsContext readsContext, final FeatureContext featureContext) {
if ( eval.isIndel() && ! eval.isComplexIndel() ) {
if ( ! ( getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples() )) {
// only if we are actually polymorphic in the subsetted samples should we count the allele
for ( Allele alt : eval.getAlternateAlleles() ) {
final int alleleSize = alt.length() - eval.getReference().length();
if ( alleleSize == 0 ) throw new GATKException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
updateLengthHistogram(eval.getReference(), alt);
}
}
}
}
Example 7
| Source File: ThetaVariantEvaluator.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 == null || !vc.isSNP() || (getWalker().ignoreAC0Sites() && vc.isMonomorphicInSamples())) {
return;
}
//this maps allele to a count
ConcurrentMap<String, Integer> alleleCounts = new ConcurrentHashMap<String, Integer>();
int numHetsHere = 0;
int numGenosHere = 0;
int numIndsHere = 0;
for (final Genotype genotype : vc.getGenotypes()) {
numIndsHere++;
if (!genotype.isNoCall()) {
//increment stats for heterozygosity
if (genotype.isHet()) {
numHetsHere++;
}
numGenosHere++;
//increment stats for pairwise mismatches
for (Allele allele : genotype.getAlleles()) {
if (allele.isCalled()) {
String alleleString = allele.toString();
alleleCounts.putIfAbsent(alleleString, 0);
alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1);
}
}
}
}
if (numGenosHere > 0) {
//only if have one called genotype at least
this.numSites++;
this.totalHet += numHetsHere / (double)numGenosHere;
//compute based on num sites
float harmonicFactor = 0;
for (int i = 1; i <= numIndsHere; i++) {
harmonicFactor += 1.0 / i;
}
this.thetaRegionNumSites += 1.0 / harmonicFactor;
//now compute pairwise mismatches
float numPairwise = 0;
int numDiffs = 0;
for (String allele1 : alleleCounts.keySet()) {
int allele1Count = alleleCounts.get(allele1);
for (String allele2 : alleleCounts.keySet()) {
if (allele1.compareTo(allele2) < 0) {
continue;
}
if (allele1 .compareTo(allele2) == 0) {
numPairwise += allele1Count * (allele1Count - 1) * .5;
}
else {
int allele2Count = alleleCounts.get(allele2);
numPairwise += allele1Count * allele2Count;
numDiffs += allele1Count * allele2Count;
}
}
}
if (numPairwise > 0) {
this.totalAvgDiffs += numDiffs / numPairwise;
}
}
}
