Code

fix: Consolidate CLI#650

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tedil merged 33 commits intomainvarfish-org/mehari:mainfrom consolidate-clivarfish-org/mehari:consolidate-cliCopy head branch name to clipboardJan 30, 2025

+1,373-293

Commits

Commits on Nov 28, 2024

• .

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  c0077ab

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Commits on Dec 16, 2024

• use TranscriptSettings in test args

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  cc28a90

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• lints

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  2031dbd

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• merge tx dbs separated by genome release

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  133e7da

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• load csq predictors depending on genome release in the server subcmd

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Commits on Dec 17, 2024

• also skip freq and clinvar dbs if assembly does not match, more info logging

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  0a29b1c

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• lint: explicit named lifetimes

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  6e43c13

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• rephrase info about skipped databases

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  1f568f8

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• check whether the predictor could be successfully instantiated, otherwise skip endpoint for respective genome_release

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  8f4decb

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• fix typo

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  b6df08c

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• rename fn seqvars to consequence

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  7f159db

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• remove databases.is_empty assertion because that is tested anyway

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Commits on Jan 2, 2025

• update sources help texts

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  d0672ab

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• fmt

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  eea025e

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• include strand in seqvars/csq

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  e93b5f1

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• add frequency endpoint (wip)

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  ff126ce

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• update 'try: …' hints to openapi

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  551d6cf

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• do not initialize predictors/annotators multiple times

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  40796ab

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• add frequency to apidocs

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  9a70495

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• also allow multiple --frequencies and --clinvar options

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• whitespace

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  b0af0ea

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• add clinvar endpoint

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  4097675

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• merge origin/main

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  720b934

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• update warning for multiple clinvar or freq dbs

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  05784eb

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• update openapi schema

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Commits on Jan 3, 2025

• update entrypoint to match new server run cli

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  f1c010f

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• fix server run clinvar docstrings

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  ee9ebf1

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• update openapi.schema.yaml accordingly

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  5fd01b5

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Commits on Jan 24, 2025

• merge origin/main

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  78d646c

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• remove unused path_db from test

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• only print hints for available endpoints

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  61ee096

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• server: add exemplary Grch38 hints

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  096c922

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• fix typo in fn name

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  fa2cbeb

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