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()];
}
