EVA-3434 Remove locus equality condition from DeprecatedVariantMongoReader #430
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| String submittedVariantContig = submittedVariant.getString(CONTIG_FIELD); | ||
| String reference = submittedVariant.getString("ref"); | ||
| String alternate = submittedVariant.getString("alt"); | ||
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| if (isSameLocation(contig, start, submittedVariantContig, submittedVariantStart, type)) { | ||
| if (contig.equals(submittedVariantContig)) { |
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removed the condition for checking the start, but was not sure if we needed to remove the contig checking as well, so left it for now
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I think we need to also remove the contig condition.
It does not make sense to check the contig if we don't check the start.
| String alternate = submittedVariant.getString("alt"); | ||
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| // Since we only need evidence that at least one submitted variant agrees | ||
| // with the deprecated RS in locus, we just return one variant record per RS |
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We should remove the part about agreeing on locus, and perhaps move the comment to above line 110 as it helps explain why we only call submittedVariantOperations.iterator().next() rather than iterating through all operations.
(This is all a bit of a faff since AFAICT we just output the rsID anyway and the whole aggregation pipeline is to confirm that the rsID was ever present for this taxonomy to begin with... but that's a separate discussion...)
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