Example #1
0
 @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());
 }
Example #2
0
 @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"));
 }
Example #3
0
    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;
    }