Fix #132: honor max_protein_sequences_per_variant in run_isovar#140
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…ces_for_variant Apply the cap inside sorted_protein_sequences_for_variant so both run_isovar and protein_sequences_from_read_evidence_generator respect it. Remove the now-redundant slice in the generator path. Before this change, ProteinSequenceCreator(max_protein_sequences_per_variant=N) and the --max-protein-sequences-per-variant CLI flag were silently ignored when used through run_isovar (the main `isovar` CLI), since that code path called sorted_protein_sequences_for_variant directly. Adds three regression tests: unit test for the cap, unit test for the None (no-cap) case, and integration test through run_isovar. All fail on the unfixed code. Fixes #132
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coverage: 92.969% (+0.05%) from 92.923% — fix-132-max-protein-sequences-cap into master |
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Summary
sorted_protein_sequences_for_variantnow applies themax_protein_sequences_per_variantcap, so bothrun_isovarand the generator code path respect it.protein_sequences_from_read_evidence_generator.run_isovar— all fail without the fix.Fixes #132
Test plan
./test.shpasses (152 tests)./lint.shpasses