Package de.charite.compbio.jannovar.hgvs.bridge

Class NucleotideChangeToGenomeVariantTranslator

java.lang.Object

de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator

public class NucleotideChangeToGenomeVariantTranslator
extends Object

Helper for converting a NucleotideChange to a GenomeVariant.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
NucleotideChangeToGenomeVariantTranslator(de.charite.compbio.jannovar.data.JannovarData jvDB, htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFasta)

Method Summary

Modifier and Type	Method	Description
de.charite.compbio.jannovar.reference.GenomeVariant	translateNucleotideVariantToGenomeVariant(de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant variant)	Shortcut to translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) with using true for the second parameter.
de.charite.compbio.jannovar.reference.GenomeVariant	translateNucleotideVariantToGenomeVariant(de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant variant, boolean autocorrect)	Translate single-change SingleAlleleNucleotideVariant into a GenomeVariant

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NucleotideChangeToGenomeVariantTranslator

public NucleotideChangeToGenomeVariantTranslator(de.charite.compbio.jannovar.data.JannovarData jvDB,
                                                 htsjdk.samtools.reference.IndexedFastaSequenceFile indexedFasta)

Method Detail

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 to translateNucleotideVariantToGenomeVariant(SingleAlleleNucleotideVariant, boolean) with using true for the second parameter.

Throws:

CannotTranslateHGVSVariant

de.charite.compbio.jannovar.annotation.InvalidGenomeVariant

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-change SingleAlleleNucleotideVariant into a GenomeVariant

Parameters:

variant - SingleAlleleNucleotideVariant to translate

autocorrect - try to auto-correct mismatching reference sequence instead of throwing CannotTranslateHGVSVariant

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 of variant or unsupported NucleotideChanges

de.charite.compbio.jannovar.annotation.InvalidGenomeVariant