Label only requested genes in scatter -g, not co-binned neighbors (gh#458)

[etal]

Summary

cnvkit scatter -c chr17:37850000-37890000 -g ERBB2 also labeled MIR4728 — a gene the user never requested — contradicting the documented behavior (doc/plots.rst: "Any other genes in the plotted region will not be shown unless also specified with -g").

Root cause

CNVkit stores gene annotation inside each bin's gene column rather than as a separate track, so one bin label can pack several comma-joined genes (e.g. "ERBB2,MIR4728"). In cnvlib/plots.py::gene_coords_by_name, bins were selected correctly by the requested name, but the region's label was then reconstructed from the union of all gene names appearing in those bins — leaking co-binned neighbors.

Fix

Restrict the reconstructed label to the requested names:

uniq_names.update(g for g in oname.split(",") if g in names)

When several genes are requested and happen to share bins, all requested names still appear. Because every selected bin necessarily contains the requested name, no region can become unlabeled.

Tests

• New CNATests::test_gene_coords_by_name (in test/test_cnvlib.py): asserts -g ERBB2 against a bin labeled "ERBB2,MIR4728" yields only ERBB2, and that requesting both names surfaces both. The test fails against the old code ('ERBB2,MIR4728' != 'ERBB2') and passes with the fix.
• Full test_cnvlib.py (30) and test_commands.py (73) pass; mypy and ruff clean.

Notes

• Plotting-label fix only — no change to .cnr/.cns/.cnn/SEG/VCF output, so no impact on downstream clinical pipelines.
• The code now matches the existing docs, so no doc change is needed.

Closes #458.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 67.81%. Comparing base (86bf4da) to head (c9d5845).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1078   +/-   ##
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  Coverage   67.81%   67.81%           
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  Files          74       74           
  Lines        7686     7686           
  Branches     1366     1366           
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  Hits         5212     5212           
  Misses       2034     2034           
  Partials      440      440           

Flag	Coverage Δ
unittests	67.81% <100.00%> (ø)

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