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hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
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Fix effect priority caching #254

Closed tavinathanson closed 7 years ago

tavinathanson commented 7 years ago

In this PR, fixes for: https://github.com/hammerlab/cohorts/issues/253 and https://github.com/hammerlab/cohorts/issues/252

Instead of an "all_effects" cache, we now remove priority filtering from the small nonsyn. cache and the larger effects cache. If all_effects is true, we don't do priority filtering after generating our collections or pulling from the cache; otherwise, we do.

Tried to test this pretty aggressively.

tavinathanson commented 7 years ago

Note that we need to clear our effects caches to make use of this PR. Should also result in a non-trivial version bump.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 52.714% when pulling e01fd5812c3a7a1f33f84a74aa6619e2e210c47c on fix_effects_caching into ea31881381e592cd26f6125a4723ccd74796ec0e on master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 52.714% when pulling b2e01a8b8371a1caa4d5a8cd9f356c0623370326 on fix_effects_caching into ea31881381e592cd26f6125a4723ccd74796ec0e on master.

tavinathanson commented 7 years ago

@jburos great idea! Just moved top_priority_maybe. Good to merge on green?

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 52.714% when pulling 84d059f7c8138d52ba09fa90b94087dfb71dedf4 on fix_effects_caching into ea31881381e592cd26f6125a4723ccd74796ec0e on master.

jburos commented 7 years ago

@tavinathanson sorry if you didn't see my 👍 -- but yep good to go whenever you are ready. Once this has been merged I will update my pending PRs to be consistent with these changes.