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opencb / cellbase

High-Performance NoSQL database and RESTful web services to access to most relevant biological data
Apache License 2.0
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fix truncation of results in phased queries where checkAminoAcidChange=TRUE #690

Open julie-sullivan opened 1 month ago

julie-sullivan commented 1 month ago

Please see Todd's document for a full description of the bug, but here is a summary:

  1. example query input: 1:100:A:G with parameters: checkAminoAcidChange = true, ignorePhase=false
  2. HGVS value is used to query results not the variant coordinates e.g. p.Met1?
  3. Query results may include more than one variant matching p.Met1?: 4. e.g. 1:100:A:G (3 trait associations) 1:101:A:G (2 trait associations) 1:101:T:C (7 trait associations)
  4. code picks the first result and ignores the rest.

Also we have a unit test but it uses mockito. Do you want it anyway?

15:90766924:T:G,15:90766927:G:T were the original problematic variants.