public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
if (reference == null) return;
// don't validate if we're a complex event
if (!isComplexIndel() && !reference.isNull() && !reference.basesMatch(getReference())) {
throw new TribbleException.InternalCodecException(
String.format(
"the REF allele is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s",
getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
}
// we also need to validate the padding base for simple indels
if (hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase)) {
throw new TribbleException.InternalCodecException(
String.format(
"the padded REF base is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s",
getChr(),
getStart(),
(char) paddedRefBase.byteValue(),
(char) getReferenceBaseForIndel().byteValue()));
}
}
