feat: dual-reference rendering for heterologous MSAs#4
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Adds variant-call ref / numbering-ref split so HIV-style alignments can color mismatches against one strain (e.g. SF162p3) while numbering the x-axis from another (e.g. HxB2). New CLI flags: --variant-ref, --numbering-ref, --show-row-labels, --tick-every, --per-panel-axes, --max-rows, --show. - fasta_panel: variant_ref/numbering_ref selection, max_rows cap, tick_every - renderer: second x-axis for dual-ref, per-panel axes, row labels - cli: kitten icat --show, BAM warn-on-fasta-only flags, max_rows - tests: dual-ref, per-panel axes, CLI flag coverage; regenerated outputs - README: dual-reference section, per-row labels, tick frequency examples
Click <8.2 requires mix_stderr=False to access result.stderr; Click 8.2+ removed that parameter and stderr capture differs. Try mix_stderr=False first, fall back to default runner, and tolerate either stderr or combined output for the kitten missing-soft-failure assertion.
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Summary
--variant-ref,--numbering-ref,--show-row-labels,--tick-every,--per-panel-axes,--max-rows,--show.Test plan
pytest tests/test_dual_ref.py tests/test_heterologous.py tests/test_per_panel_axes.py tests/test_cli.py tests/test_fasta.pytests/output/*.png(dual_ref, per_panel_axes, row_labels)tview <fasta> --variant-ref SF162p3 --numbering-ref HxB2 --show-row-labels --tick-every 25--showinvokeskitten icatonly when terminal supports it (only works for ghostty)