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Doc changes for alt_allele_prob_file and est_pheno_penetrance_prob#220

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gregorgorjanc merged 4 commits into
AlphaGenes:gg/docPolishfrom
RosCraddock:DocChanges
Feb 17, 2026
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Doc changes for alt_allele_prob_file and est_pheno_penetrance_prob#220
gregorgorjanc merged 4 commits into
AlphaGenes:gg/docPolishfrom
RosCraddock:DocChanges

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  • Updated the alternative allele file format description and examples.
  • Added description for estimation of the phenotype penetrance probability estimation
  • Removed associated TODOs

…nce estimation

- Updated the alternative allele file format description and examples.
- Added description for estimation of the phenotype penetrance probability estimation
- Removed associated todos
Comment thread docs/source/usage.rst
are estimated as the proportion of mismatches between observed and inferred states.

TODO: Say something about penetrance probabilities estimation (Ros)
Phenotype penetrance probabilities (using ``est_pheno_penetrance_prob``) are estimated

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Suggested change
Phenotype penetrance probabilities (using ``est_pheno_penetrance_prob``) are estimated
Phenotype penetrance probabilities (using ``-est_pheno_penetrance_prob``) are estimated

@gregorgorjanc

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Thanks @RosCraddock! Will merge this in and polish on my end to match the style with other file descriptions.

@gregorgorjanc gregorgorjanc merged commit a77650d into AlphaGenes:gg/docPolish Feb 17, 2026
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