public boolean isHigherImpactThan(SnpEffEffect other) {
// If one effect is within a coding gene and the other is not, the effect that is
// within the coding gene has higher impact:
if (isCoding() && !other.isCoding()) {
return true;
} else if (!isCoding() && other.isCoding()) {
return false;
}
// Otherwise, both effects are either in or not in a coding gene, so we compare the impacts
// of the effects themselves. Effects with the same impact are tie-broken using the
// functional class of the effect:
if (impact.isHigherImpactThan(other.impact)) {
return true;
} else if (impact.isSameImpactAs(other.impact)) {
return functionalClass.isHigherPriorityThan(other.functionalClass);
}
return false;
}
@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;
}
private void parseEffectMetadata(String[] effectMetadata) {
if (effectMetadata.length != EXPECTED_NUMBER_OF_METADATA_FIELDS) {
if (effectMetadata.length == NUMBER_OF_METADATA_FIELDS_UPON_EITHER_WARNING_OR_ERROR) {
parseError(
String.format(
"SnpEff issued the following warning or error: \"%s\"",
effectMetadata[SNPEFF_WARNING_OR_ERROR_FIELD_UPON_SINGLE_ERROR]));
} else if (effectMetadata.length == NUMBER_OF_METADATA_FIELDS_UPON_BOTH_WARNING_AND_ERROR) {
parseError(
String.format(
"SnpEff issued the following warning: \"%s\", and the following error: \"%s\"",
effectMetadata[SNPEFF_WARNING_FIELD_UPON_BOTH_WARNING_AND_ERROR],
effectMetadata[SNPEFF_ERROR_FIELD_UPON_BOTH_WARNING_AND_ERROR]));
} else {
parseError(
String.format(
"Wrong number of effect metadata fields. Expected %d but found %d",
EXPECTED_NUMBER_OF_METADATA_FIELDS, effectMetadata.length));
}
return;
}
// The impact field will never be empty, and should always contain one of the enumerated
// values:
try {
impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]);
} catch (IllegalArgumentException e) {
parseError(
String.format(
"Unrecognized value for effect impact: %s",
effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]));
}
// The functional class field will be empty when the effect has no functional class associated
// with it:
if (effectMetadata[InfoFieldKey.FUNCTIONAL_CLASS_KEY.getFieldIndex()].trim().length() > 0) {
try {
functionalClass =
EffectFunctionalClass.valueOf(
effectMetadata[InfoFieldKey.FUNCTIONAL_CLASS_KEY.getFieldIndex()]);
} catch (IllegalArgumentException e) {
parseError(
String.format(
"Unrecognized value for effect functional class: %s",
effectMetadata[InfoFieldKey.FUNCTIONAL_CLASS_KEY.getFieldIndex()]));
}
} else {
functionalClass = EffectFunctionalClass.NONE;
}
codonChange = effectMetadata[InfoFieldKey.CODON_CHANGE_KEY.getFieldIndex()];
aminoAcidChange = effectMetadata[InfoFieldKey.AMINO_ACID_CHANGE_KEY.getFieldIndex()];
geneName = effectMetadata[InfoFieldKey.GENE_NAME_KEY.getFieldIndex()];
geneBiotype = effectMetadata[InfoFieldKey.GENE_BIOTYPE_KEY.getFieldIndex()];
// The coding field will be empty when SnpEff has no coding info for the effect:
if (effectMetadata[SNPEFF_CODING_FIELD_INDEX].trim().length() > 0) {
try {
coding = EffectCoding.valueOf(effectMetadata[SNPEFF_CODING_FIELD_INDEX]);
} catch (IllegalArgumentException e) {
parseError(
String.format(
"Unrecognized value for effect coding: %s",
effectMetadata[SNPEFF_CODING_FIELD_INDEX]));
}
} else {
coding = EffectCoding.UNKNOWN;
}
transcriptID = effectMetadata[InfoFieldKey.TRANSCRIPT_ID_KEY.getFieldIndex()];
exonID = effectMetadata[InfoFieldKey.EXON_ID_KEY.getFieldIndex()];
}