Fix for events not in minimal representation #8567
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@davidbenjamin Do you have time for a review here? Or can you please suggest someone? Thanks! |
davidbenjamin
requested changes
Nov 2, 2023
| * @return pair of alleles in minimal representation | ||
| */ | ||
| private static Pair<Allele, Allele> makeMinimalRepresentation(Allele ref, Allele alt) { | ||
| Utils.validateArg(!Arrays.equals(ref.getBases(), alt.getBases()), "ref and alt alleles are identical"); |
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Use Allele::baseMatch
| refAllele = ref; | ||
| altAllele = alt; | ||
| } else { | ||
| Pair<Allele, Allele> minimalAlleles = makeMinimalRepresentation(ref, alt); |
| byte[] newRefBases = ref.getBases(); | ||
| byte[] newAltBases = alt.getBases(); | ||
| while (newRefBases.length != 1 && newAltBases.length != 1 && !differentLastBase(newRefBases, newAltBases)) { | ||
| newRefBases = Arrays.copyOf(ref.getBases(), ref.length() - 1); |
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The array operations shouldn't be inside the loop. First calculate how many bases are identical at the end, then trim the base arrays.
| * @param alt allele not in minimal representation | ||
| * @return pair of alleles in minimal representation | ||
| */ | ||
| private static Pair<Allele, Allele> makeMinimalRepresentation(Allele ref, Allele alt) { |
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Because it's much more common that the allele representation is already minimal, it's worth checking for this and just returning the original ref and alt if possible without needing to call Allele.create.
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Thanks @davidbenjamin, back to you! |
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A non-minimally represented allele in dbsnp was causing GenotypeGVCFs to throw an error. This PR fixes this and removes a TODO.