Fix ONT bam file ML/MM parsing for h and m modifications - #112
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When a read carries both 5hmC (C+h) and 5mC (C+m) modifications with different position counts, the ML probability array was sliced using MM_pos * nr_MM_vals as the offset — implicitly assuming equal block sizes. This caused the guard condition to fail (e.g. 611 >= 956 is false for real ONT reads with ~133 C+h and ~478 C+m positions), leaving ML_str un-trimmed and triggering a size-mismatch throw in parse_np_fields_by_mod. Fix: compute ml_offset as the cumulative sum of position counts from all prior MM sections before overwriting MM_str. Matches the SAM spec that ML values are ordered identically to MM positions across all sections. Add test_ont_ml.cpp with 5 unit tests covering unequal counts (both orderings), equal counts, and only-m cases. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Works for me. Claude hallusinated the new build target in setup.py (which is not modified)