@Override
public List<String> getKeyNames() {
return Arrays.asList(
InfoFieldKey.EFFECT_KEY.getKeyName(),
InfoFieldKey.IMPACT_KEY.getKeyName(),
InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName(),
InfoFieldKey.CODON_CHANGE_KEY.getKeyName(),
InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(),
InfoFieldKey.GENE_NAME_KEY.getKeyName(),
InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(),
InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(),
InfoFieldKey.EXON_ID_KEY.getKeyName());
}
@Override
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(
new VCFInfoHeaderLine(
InfoFieldKey.EFFECT_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"),
new VCFInfoHeaderLine(
InfoFieldKey.IMPACT_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Impact of the highest-impact effect resulting from the current variant "
+ Arrays.toString(EffectImpact.values())),
new VCFInfoHeaderLine(
InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Functional class of the highest-impact effect resulting from the current variant: "
+ Arrays.toString(EffectFunctionalClass.values())),
new VCFInfoHeaderLine(
InfoFieldKey.CODON_CHANGE_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Old/New codon for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(
InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Old/New amino acid for the highest-impact effect resulting from the current variant (in HGVS style)"),
new VCFInfoHeaderLine(
InfoFieldKey.GENE_NAME_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Gene name for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(
InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Gene biotype for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(
InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Transcript ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(
InfoFieldKey.EXON_ID_KEY.getKeyName(),
1,
VCFHeaderLineType.String,
"Exon ID for the highest-impact effect resulting from the current variant"));
}
public Map<String, Object> getAnnotations() {
Map<String, Object> annotations =
new LinkedHashMap<String, Object>(Utils.optimumHashSize(InfoFieldKey.values().length));
addAnnotation(annotations, InfoFieldKey.EFFECT_KEY.getKeyName(), effect.toString());
addAnnotation(annotations, InfoFieldKey.IMPACT_KEY.getKeyName(), impact.toString());
addAnnotation(
annotations, InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName(), functionalClass.toString());
addAnnotation(annotations, InfoFieldKey.CODON_CHANGE_KEY.getKeyName(), codonChange);
addAnnotation(annotations, InfoFieldKey.AMINO_ACID_CHANGE_KEY.getKeyName(), aminoAcidChange);
addAnnotation(annotations, InfoFieldKey.GENE_NAME_KEY.getKeyName(), geneName);
addAnnotation(annotations, InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), geneBiotype);
addAnnotation(annotations, InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), transcriptID);
addAnnotation(annotations, InfoFieldKey.EXON_ID_KEY.getKeyName(), exonID);
return annotations;
}