private List<SnpEffEffect> parseSnpEffRecord(VariantContext snpEffRecord) {
List<SnpEffEffect> parsedEffects = new ArrayList<SnpEffEffect>();
Object effectFieldValue = snpEffRecord.getAttribute(SNPEFF_INFO_FIELD_KEY);
if (effectFieldValue == null) {
return parsedEffects;
}
// The VCF codec stores multi-valued fields as a List<String>, and single-valued fields as a
// String.
// We can have either in the case of SnpEff, since there may be one or more than one effect in
// this record.
List<String> individualEffects;
if (effectFieldValue instanceof List) {
individualEffects = (List<String>) effectFieldValue;
} else {
individualEffects = Arrays.asList((String) effectFieldValue);
}
for (String effectString : individualEffects) {
String[] effectNameAndMetadata = effectString.split(SNPEFF_EFFECT_METADATA_DELIMITER);
if (effectNameAndMetadata.length != 2) {
logger.warn(
String.format(
"Malformed SnpEff effect field at %s:%d, skipping: %s",
snpEffRecord.getChr(), snpEffRecord.getStart(), effectString));
continue;
}
String effectName = effectNameAndMetadata[0];
String[] effectMetadata =
effectNameAndMetadata[1].split(SNPEFF_EFFECT_METADATA_SUBFIELD_DELIMITER, -1);
SnpEffEffect parsedEffect = new SnpEffEffect(effectName, effectMetadata);
if (parsedEffect.isWellFormed()) {
parsedEffects.add(parsedEffect);
} else {
logger.warn(
String.format(
"Skipping malformed SnpEff effect field at %s:%d. Error was: \"%s\". Field was: \"%s\"",
snpEffRecord.getChr(),
snpEffRecord.getStart(),
parsedEffect.getParseError(),
effectString));
}
}
return parsedEffects;
}
