Add Markov quality model test coverage and fix invalid test data#270
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test_qual_score_models.py: - Fix two tests that used -1 as a quality score key in position_distributions (invalid data that bypassed real validation); replace with valid scores - Add 11 new tests covering the previously untested Markov chain path: transition chain is exercised, fallback to marginal for unknown q_prev, wrong transition_distributions length raises, out-of-range score clamping, length=0/1 edge cases, read-length interpolation via _position_index_for_length test_error_models.py: - Remove two stub tests that imported from error_models.MarkovQualityModel (a dead TODO class never called at runtime); they passed unconditionally and gave false confidence about the real model test_markov_utils.py (new): - 36 tests covering all previously untested functions in markov_utils.py: _down_bin_quality (6), compute_initial_distribution (4), compute_position_distributions (4), compute_transition_distributions (5), read_quality_lists (6), build_markov_model (3) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Finished combing through the tests! The changes all make sense to me. |
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test_qual_score_models.py:
test_error_models.py:
test_markov_utils.py (new):