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Anja 92/sv overlap endpoint

Marek Szuba requested to merge github/fork/at7/anja_92/sv_overlap_endpoint into master

Created by: at7


This is a bug fix: The overlap endpoint for structural_variation never worked the way it was implemented. There was a change for the somatic_structural_variation routine. I updated the structural_variation routine accordingly. There are SO terms for the variant consequence and for the variant class. For structural variants we have only SO terms for the variant class. We could consider to have a filter for variant class in the future. But this is beyond the scope of this bug fix.

Use case

get all structural variants or all somatic structural variants in a region


bug fix

Possible Drawbacks



I provided 2 more tests to ensure that structural_variation and somatic_structural_variation return data.

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