public final class VariantNormalizer extends Object
Constructor and Description |
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VariantNormalizer(String fastaPath)
Construct new variant normalizer object
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Modifier and Type | Method and Description |
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VariantDescription |
normalizeInsertion(VariantDescription desc)
Normalize a variant given as a start coordinate, reference, and variant sequence
However, leave the leftmost base intact in the case so insertions have a REF base.
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VariantDescription |
normalizeVariant(VariantDescription desc)
Normalize a variant given as a start coordinate, reference, and variant sequence
The chromosome is given by its name, position is an 0-based integer, reference and variant are given as sequence.
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public VariantNormalizer(String fastaPath) throws JannovarVarDBException
fastaPath
- Path to indexed FASTA fileJannovarVarDBException
- On problems with opening the FASTA/FAI filepublic VariantDescription normalizeVariant(VariantDescription desc)
public VariantDescription normalizeInsertion(VariantDescription desc)
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