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…-workflow-modules Adjust plotting modules for spatial and latent workflows
…ons-as-grey Mask and grey-out positions outside reads in rolling NN clustermaps
…for-preprocessing Add option to generate mismatch clustermaps that exclude annotated modification sites
…requency_sites-for-dynamic-labeling Flag variable mismatch sites using per-position Q-score error rates
…-sites Ignore ambiguous GpC_CpG sites when excluding GpC/CpG in sequence clustermaps
…ncy-plotting Plot mismatch base frequencies by position (with optional mod-site exclusion)
…y-plotting-logic Ignore strand-specific self-base mismatches in mismatch frequency plots
…modules Add structured logging across plotting modules
…ics-to-var Add per-reference base quality and error stats
…-for-variant-types Add optional quality-normalized z-score panel to mismatch frequency plots
…ariant-frequencies Add per-reference mismatch z-score summary CSV with max-zscore base columns
…-scores-by-reference Add per-reference pooled-samples handling in mismatch base frequency plots
…r-nan-positions Add `max_nan_run` to stop zero-Hamming segment expansion across consecutive NaNs
…ior-in-clustermap Add rolling NN panel to zero-Hamming span clustermap with barplots and read-span masking
…ior-in-clustermap Pass rolling NN obsm key to zero-Hamming plot and enable NN panel in chimeric_adata
…anel in chimeric_adata"
…layer-behavior-in-clustermap Revert "Pass rolling NN obsm key to zero-Hamming plot and enable NN panel in chimeric_adata"
…plots and read-span masking"
…layer-behavior-in-clustermap Revert "Add rolling NN panel to zero-Hamming span clustermap with barplots and read-span masking"
…ling-nearest-neighbor Add rolling NN two-layer clustermap plotting with read-span masking
…atches-clustermap Align chimeric rolling NN two-layer plots
Update AGENTS.md
chimeric plotting
Chimeric fixes
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