main <- dev #796
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main <- dev #796
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* Bump requirements * add validation * format
* Bump requirements * add validation * format * Fix syntax
* add allele registry step in update vat with samples task * shh * existing tests pass * fix test deps * test * annotation_dependencies * ruff * take out the zero check * fix requirements new task name * move vep into new variants task * only annotate lookup from callset_ht * clean up mocks * r * working * working? * not that * minor changes and test cases * most recent script * working version * fix the test * implement ht chunking * fix patches * fix patches * register now yields id map of returned caids * r * fix some tests * return a hail table instead * use __str__ * log to track variants we can't map back * move to gcs with flag * union ar_ht instead of a bunch of left joins to prevent CAID, CAID_1, CAID_2... * cleaner * it is all coming together now ' * gnomad ids for 37' * use genomicalleles and gnomad ids * secrets * secret * move stuff out of environment file * add more logging * fix test * fix the other test * ruff * test * comments * o
* Finish validity check test * ruff * update dbnsfp field * More types * more types * ugh * twiddle it back * update type * more tweaks * lint * fix floats * decompose * ruff formatg * Update compare_globals_test.py
* exclude unknowns from sex check * add a test * ruff
jklugherz
approved these changes
May 28, 2024
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