SACGF / SACGF/variantgrid

Search for del/dups that failed liftover provides unhelpful search results.

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#1,445 1 comment 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
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Python
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Description

Emma found while testing search functionality for deletions and duplications.

When searching for a deletion or duplication, if no exact matches are present in the database, then the search result will return overlapping variants.

If a variant is imported in one genome build but cannot be successfully lifted over to the other genome build, search will return a single result for the genome build with the variant present, but will also return overlapping variants in the genome build to which liftover failed.

Given that there is a match for the variant, it doesn't seem appropriate to display overlapping variants in the failed genome build in this case.

This is a rare edge case that doesn't need to be addressed for the Shariant BCFtools release.

Potentially only noticed now as search previously had a bug (That has now been fixed) that lead to search results failing in both genome builds if one genome build failed liftover (sacgf/variantgrid#1105).

Shariant Test currently doesn't have admin lab loaded and we have a freeze on importing variants, but will update issue with additional info and examples when available.

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