public class InheritanceVariantContext
extends htsjdk.variant.variantcontext.VariantContext
VariantContext
for the
InheritanceCompatibilityChecker
.Modifier and Type | Method and Description |
---|---|
void |
addMatchInheritance(ModeOfInheritance matchInheritance)
Add a mode of inheritance to this variant.
|
Genotype |
getGenotype(Person p)
|
Set<ModeOfInheritance> |
getMatchedModesOfInheritance()
getter of
matchedModesOfInheritance . |
Genotype |
getSingleSampleGenotype()
|
boolean |
isMatchInheritance()
Getter of
matchedModesOfInheritance . |
calcVCFGenotypeKeys, emptyID, extraStrictValidation, filtersWereApplied, fullyDecode, getAllele, getAllele, getAlleleIndex, getAlleleIndices, getAlleles, getAltAlleleWithHighestAlleleCount, getAlternateAllele, getAlternateAlleles, getAttribute, getAttribute, getAttributeAsBoolean, getAttributeAsDouble, getAttributeAsInt, getAttributeAsList, getAttributeAsString, getAttributes, getCalledChrCount, getCalledChrCount, getCalledChrCount, getCalledChrCount, getChr, getCommonInfo, getContig, getEnd, getFilters, getFiltersMaybeNull, getGenotype, getGenotype, getGenotypes, getGenotypes, getGenotypes, getGenotypesOrderedBy, getGenotypesOrderedByName, getGLIndecesOfAlternateAllele, getHetCount, getHomRefCount, getHomVarCount, getID, getIndelLengths, getLog10PError, getMaxPloidy, getMixedCount, getNAlleles, getNoCallCount, getNSamples, getPhredScaledQual, getReference, getSampleNames, getSampleNamesOrderedByName, getSource, getStart, getType, hasAllele, hasAllele, hasAlternateAllele, hasAlternateAllele, hasAttribute, hasGenotype, hasGenotypes, hasGenotypes, hasID, hasLog10PError, hasSameAllelesAs, hasSameAlternateAllelesAs, hasSymbolicAlleles, hasSymbolicAlleles, isBiallelic, isComplexIndel, isFiltered, isFullyDecoded, isIndel, isMixed, isMNP, isMonomorphicInSamples, isNotFiltered, isPointEvent, isPolymorphicInSamples, isSimpleDeletion, isSimpleIndel, isSimpleInsertion, isSNP, isStructuralIndel, isSymbolic, isSymbolicOrSV, isVariant, subContextFromSample, subContextFromSamples, subContextFromSamples, toString, toStringDecodeGenotypes, toStringWithoutGenotypes, validateAlternateAlleles, validateChromosomeCounts, validateReferenceBases, validateRSIDs
public void addMatchInheritance(ModeOfInheritance matchInheritance)
Add a mode of inheritance to this variant.
matchInheritance
- A mode of inheritance that matches to this variant.public Genotype getSingleSampleGenotype()
Genotype
stored in the
VariantContext
public Set<ModeOfInheritance> getMatchedModesOfInheritance()
matchedModesOfInheritance
.Set
with ModeOfInheritance
that matches with this
variant.public boolean isMatchInheritance()
matchedModesOfInheritance
.true
if the InheritanceVariantContext
matches
the ModeOfInheritance
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