Add python script to our repo #8282
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RoriCremer
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RoriCremer
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Apr 24, 2023
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8282 +/- ##
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Coverage ? 86.097%
Complexity ? 35607
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Files ? 2197
Lines ? 167119
Branches ? 18007
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Hits ? 143884
Misses ? 16802
Partials ? 6433 |
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| def import_gvs(refs: 'List[List[str]]', |
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Weren't we going to rename this something other than import_gvs at this stage? It's obviously not necessary, but I thought I remember the team discussing that
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| def import_gvs(argsfn, vds_path, references_path, temp_path): | |||
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see my comment above about potentially renaming this function from import_gvs to something else. It is not strictly necessary, but if it were to be done this is the ticket that we were going to do it in, I believe
gbggrant
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Apr 28, 2023
gbggrant
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mcovarr
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May 4, 2023
koncheto-broad
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The first step of taking this code from the Hail team is just pasting it into our repo
Successful run:
https://job-manager.dsde-prod.broadinstitute.org/jobs/49d62f48-2dee-417c-aa65-411cbe47be17
GvsQuickstartHailIntegration--we remove the whl from the integration test---sure seems like we wont need one going forward!
Another ticket will be made for these next steps:
Likely this will need to end up in our docker image and the WDL that creates the Avro files can make a version of the input for this scripts instead
Next we will want to remove the Tranches calculations and instead of that value passed in as yet another parameter
Phasing and dropping GQ0