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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 insertion with n consequence type #672

Open awab-ahmed opened 1 year ago

awab-ahmed commented 1 year ago

4.12.5 introduced a bug where insertion variants > 50bp with N in the reference are classified as MNVs and therefore their consequeneTypes are miscalculated.

E.g of variant: 11:68410141:N:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGN

In this PR the conditions in VariantAnnotationUtils.getVariantType are changed so that such variants are classified as insertions so that the correct ConsequenceTypeCalculator gets assigned.