VS-757 - Use JASIX to make sub-jsons of annotated output of Nirvana #8133
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…re tractable for our python scripts.
gbggrant
commented
Dec 16, 2022
gbggrant
commented
Dec 16, 2022
gbggrant
commented
Dec 16, 2022
gbggrant
commented
Dec 16, 2022
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8133 +/- ##
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Coverage ? 86.241%
Complexity ? 35194
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Files ? 2173
Lines ? 165045
Branches ? 17794
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Hits ? 142336
Misses ? 16384
Partials ? 6325 |
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LGTM! Have any numbers on the performance improvement? It wasn't easy to see an old run before Jasix that would be a good 1-to-1 comparison. |
koncheto-broad
approved these changes
Dec 16, 2022
scripts/variantstore/wdl/extract/create_genes_bqloadjson_from_annotations.py
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scripts/variantstore/wdl/extract/create_vt_bqloadjson_from_annotations.py
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gbggrant
commented
Dec 19, 2022
This was referenced Mar 17, 2023
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This PR uses Nirvana's JASIX parser to break the annotated output of Nirvana into a genes and positions json which are then parsed by the corresponding python methods. This improves performance significantly.
Successful workflow here:
https://app.terra.bio/#workspaces/gvs-dev/GVS%20Quickstart%20v3%20ggrant/job_history/14d2d1cf-3a2a-42e0-8542-c70edd2133e5