Feature/binned quality scoring - #304
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TraditionalQualityModel now accepts an optional quality_bins parameter that snaps sampled scores to the nearest discrete bin using vectorized np.searchsorted, matching how NovaSeq/NextSeq 2000 instruments emit only a small set of Phred values (e.g. Q2/Q12/Q23/Q37). The runner passes allowed_bins through so both Markov and traditional models produce realistically binned output when bins are specified. - Add quality_bins to TraditionalQualityModel.__init__ and get_quality_scores() - Pass allowed_bins to TraditionalQualityModel in model_qual_score runner - Expose _down_bin_quality as public down_bin_quality in markov_utils - Add QUALITY_PRESETS dict in neat/quality_score_modeling/presets.py (novaseq, nextseq2000, nextseq500) - Add --quality-preset CLI flag to neat model-qual-score; implies --markov - Fix stale -Q help text in model_sequencing_error CLI - Add TraditionalQualityModel binning tests + preset data/CLI tests Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add a "Binned quality scoring" subsection to neat model-qual-score showing how to use --quality-preset (novaseq, nextseq2000, nextseq500) and explicit -Q bin lists for instruments that emit discrete Phred levels. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Updates to renable binned scoring, now that the other things are fixed. Binned scoring requires user input for NEAT to know that bins are present. See README for details.