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Adapt hl.de_novo function#760

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KoalaQin merged 59 commits intomainbroadinstitute/gnomad_methods:mainfrom qh/de_novobroadinstitute/gnomad_methods:qh/de_novoCopy head branch name to clipboardFeb 12, 2025

+858-1

Commits

Commits on Jan 21, 2025

• Add function to compute post probability of de novos

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Commits on Jan 24, 2025

• confidence and fail check function

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Commits on Jan 28, 2025

• Modify de novo function

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Commits on Jan 29, 2025

• black formatting

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• Reformat docstring

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• Change the citation

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Commits on Jan 30, 2025

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• Transpose the thresholds table

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• merge origin changes

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Commits on Jan 31, 2025

• Add a call_de_novo function

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• Formatting

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• isort

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Commits on Feb 3, 2025

• Add test module for de novo functions

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• small formatting

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Commits on Feb 5, 2025

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• Reformat docstring and move helper functions

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• Correct the confidence errors

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• Move is_de_novo

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• reST hyperlink format in docstring

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Commits on Feb 6, 2025

• Add test

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• remove imports

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• docstring typo

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Commits on Feb 7, 2025

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• Docstring changes

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• Merge suggestions

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• A small change

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• Add error case

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• Change indel HIGH code

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• typo

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Commits on Feb 9, 2025

• Remove extra

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• Adjust table

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Commits on Feb 10, 2025

• Put copy state function back

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• Add expected error case

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• Minor number change

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Commits on Feb 11, 2025

• Make a fixture for pytest

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• Add more cases

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• Merge remote-tracking branch 'origin/main' into qh/de_novo

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• Docstring format

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Commits on Feb 12, 2025

• Address review comments

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• Remove unused imports

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• specify XY only

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