public class NucleotideChangeToGenomeVariantTranslator extends Object
NucleotideChange
to a GenomeVariant
.Constructor and Description |
---|
NucleotideChangeToGenomeVariantTranslator(JannovarData jvDB,
htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFasta) |
Modifier and Type | Method and Description |
---|---|
GenomeVariant |
translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant variant)
Shortcut to
translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) with using
true for the second parameter. |
GenomeVariant |
translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant variant,
boolean autocorrect)
Translate single-change
SingleAlleleNucleotideVariant into a GenomeVariant |
public NucleotideChangeToGenomeVariantTranslator(JannovarData jvDB, htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFasta)
public GenomeVariant translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant variant) throws CannotTranslateHGVSVariant
translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean)
with using
true
for the second parameter.CannotTranslateHGVSVariant
public GenomeVariant translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant variant, boolean autocorrect) throws CannotTranslateHGVSVariant
SingleAlleleNucleotideVariant
into a GenomeVariant
variant
- SingleAlleleNucleotideVariant
to translateautocorrect
- try to auto-correct mismatching reference sequence instead of throwing
CannotTranslateHGVSVariant
GenomeVariant
resulting from the conversion, possibly annotated with some warning messagesCannotTranslateHGVSVariant
- in the case of problems such as more than one entry in the allele of variant
or
unsupported NucleotideChange
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