openvax / isovar / 24486760182

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Fix: honor max_protein_sequences_per_variant in sorted_protein_sequences_for_variant (#140)

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

3 of 3 new or added lines in 2 files covered. (100.0%)

2023 of 2176 relevant lines covered (92.97%)

2.79 hits per line