Feature/expand phenopackets - Builds on top of `feature/preprocessing-columns`#6

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VarenyaJ merged 39 commits intodevelopfrom

feature/expand-phenopackets

Aug 15, 2025

Commits on Aug 5, 2025

Commits on Aug 7, 2025

Commits on Aug 8, 2025

Commits on Aug 11, 2025

refactor(mapper): attempt to restructure DefaultMapper into modular, testable components and align interface
VarenyaJ
committed
refactor(cli, mapper): align CLI with new DefaultMapper API and preserve test output
VarenyaJ
committed
Ruff check and formatting
VarenyaJ
committed
Have the CLI be forgiving (accept `16` and normalize to `chr16`) by adding a tiny normalization in `DefaultMapper.parse_genotype_row` before constructing the `Genotype`
VarenyaJ
committed
Revise the CLI forgiveness for chromosome entry
VarenyaJ
committed
fix(mapper): emit canonical HGVS without optional 'chr' prefix
VarenyaJ
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tests: draft focused unit tests for mapper & main helpers; adjust HGVS output; cleanup
VarenyaJ
committed
refactor(mapper): split `construct_phenopacket_for_patient` into helpers; canonicalize HGVS output; tidy tests
VarenyaJ
committed

Commits on Aug 15, 2025