Class NucleotideChangeToGenomeVariantTranslator
- java.lang.Object
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- de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator
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public class NucleotideChangeToGenomeVariantTranslator extends Object
Helper for converting aNucleotideChange
to aGenomeVariant
.- Author:
- Manuel Holtgrewe
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Constructor Summary
Constructors Constructor Description NucleotideChangeToGenomeVariantTranslator(de.charite.compbio.jannovar.data.JannovarData jvDB, htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFasta)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description de.charite.compbio.jannovar.reference.GenomeVariant
translateNucleotideVariantToGenomeVariant(de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant variant)
Shortcut totranslateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean)
with usingtrue
for the second parameter.de.charite.compbio.jannovar.reference.GenomeVariant
translateNucleotideVariantToGenomeVariant(de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant variant, boolean autocorrect)
Translate single-changeSingleAlleleNucleotideVariant
into aGenomeVariant
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Method Detail
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translateNucleotideVariantToGenomeVariant
public de.charite.compbio.jannovar.reference.GenomeVariant translateNucleotideVariantToGenomeVariant(de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant variant) throws CannotTranslateHGVSVariant, de.charite.compbio.jannovar.annotation.InvalidGenomeVariant
Shortcut totranslateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean)
with usingtrue
for the second parameter.- Throws:
CannotTranslateHGVSVariant
de.charite.compbio.jannovar.annotation.InvalidGenomeVariant
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translateNucleotideVariantToGenomeVariant
public de.charite.compbio.jannovar.reference.GenomeVariant translateNucleotideVariantToGenomeVariant(de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant variant, boolean autocorrect) throws CannotTranslateHGVSVariant, de.charite.compbio.jannovar.annotation.InvalidGenomeVariant
Translate single-changeSingleAlleleNucleotideVariant
into aGenomeVariant
- Parameters:
variant
-SingleAlleleNucleotideVariant
to translateautocorrect
- try to auto-correct mismatching reference sequence instead of throwingCannotTranslateHGVSVariant
- Returns:
GenomeVariant
resulting from the conversion, possibly annotated with some warning messages- Throws:
CannotTranslateHGVSVariant
- in the case of problems such as more than one entry in the allele ofvariant
or unsupportedNucleotideChange
sde.charite.compbio.jannovar.annotation.InvalidGenomeVariant
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