public final class AlleleMatcher extends Object
Constructor and Description |
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AlleleMatcher(String pathFasta)
Construct GenotypeMatcher
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Modifier and Type | Method and Description |
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Collection<GenotypeMatch> |
matchGenotypes(htsjdk.variant.variantcontext.VariantContext obsVC,
htsjdk.variant.variantcontext.VariantContext dbVC)
Match genotypes of two
VariantContext s
Indels will be left-shifted and normalized when necessary |
Collection<GenotypeMatch> |
positionOverlaps(htsjdk.variant.variantcontext.VariantContext obsVC,
htsjdk.variant.variantcontext.VariantContext dbVC)
Pair genotypes of two
VariantContext s based on their position, regardless of their genotype
In the end, all genotypes will be matched regardless of matching alleles, such that later the "best" (e.g., the
highest frequency one) can be used for annotating a variant. |
public AlleleMatcher(String pathFasta) throws JannovarVarDBException
pathFasta
- Path to FAI-indexed FASTA fileJannovarVarDBException
- On problems with loading the FASTA/FAI filepublic Collection<GenotypeMatch> matchGenotypes(htsjdk.variant.variantcontext.VariantContext obsVC, htsjdk.variant.variantcontext.VariantContext dbVC)
VariantContext
s
Indels will be left-shifted and normalized when necessaryobsVC
- VariantContext
describing the observed variantdbVC
- VariantContext
describing the database variantCollection
of GenotypeMatch
es for the two variantspublic Collection<GenotypeMatch> positionOverlaps(htsjdk.variant.variantcontext.VariantContext obsVC, htsjdk.variant.variantcontext.VariantContext dbVC)
VariantContext
s based on their position, regardless of their genotype
In the end, all genotypes will be matched regardless of matching alleles, such that later the "best" (e.g., the
highest frequency one) can be used for annotating a variant.obsVC
- VariantContext
describing the observed variantdbVC
- VariantContext
describing the database variantCollection
of GenotypeMatch
es for the two variantsCopyright © 2016. All rights reserved.