de.charite.compbio.jannovar.annotation

Class VariantAnnotator

java.lang.Object

de.charite.compbio.jannovar.annotation.VariantAnnotator

public final class VariantAnnotator
extends Object

Main driver class for annotating variants. Given, a chromosome map, objects of this class can be used to annotate variants identified by a genomic position (chr, pos), a reference, and an alternative nucleotide String.

Author:

Manuel Holtgrewe, Marten Jaeger, Peter N Robinson

Constructor Summary

Constructors

Constructor and Description
VariantAnnotator(ReferenceDictionary refDict, com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap, AnnotationBuilderOptions options) Construct new VariantAnnotator, given a chromosome map.

Method Summary

Modifier and Type	Method and Description
VariantAnnotations	buildAnnotations(GenomeVariant change) Main entry point to getting Annovar-type annotations for a variant identified by chromosomal coordinates.
VariantAnnotations	buildAnnotations(int chr, int position, String ref, String alt, PositionType posType) Convenience function for obtaining an VariantAnnotations from genome change in primitive types.

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantAnnotator

public VariantAnnotator(ReferenceDictionary refDict,
                        com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
                        AnnotationBuilderOptions options)

Construct new VariantAnnotator, given a chromosome map.

Parameters:

refDict - ReferenceDictionary with information about the genome.

chromosomeMap - chromosome map to use for the annotator.

options - configuration to use for building the annotations

Method Detail

buildAnnotations

public VariantAnnotations buildAnnotations(int chr,
                                           int position,
                                           String ref,
                                           String alt,
                                           PositionType posType)
                                    throws AnnotationException

Convenience function for obtaining an VariantAnnotations from genome change in primitive types. Forwards to buildAnnotations(int, int, String, String, PositionType) and we recommend to use this function directly.

Parameters:

position - The start position of the variant on this chromosome (one-based numbering)

ref - String representation of the reference sequence affected by the variant

alt - String representation of the variant (alt) sequence

posType - the position type to use

Returns:

VariantAnnotations for the given genome change

Throws:

AnnotationException - on problems building the annotation list

buildAnnotations

public VariantAnnotations buildAnnotations(GenomeVariant change)
                                    throws AnnotationException

Main entry point to getting Annovar-type annotations for a variant identified by chromosomal coordinates. When we get to this point, the client code has identified the right chromosome, and we are provided the coordinates on that chromosome.

Parameters:

change - the GenomeVariant to annotate

Returns:

VariantAnnotations for the genome change

Throws:

AnnotationException - on problems building the annotation list