diagram: --gene label filter, directional thresholds, graceful reversed intervals

[etal]

Summary

Extends cnvkit.py diagram with finer control over gene labeling, plus a robustness fix for reverse-oriented input intervals.

• --gene MYC,ERBB2 — label only the named genes among those passing the threshold, dropping co-binned neighbors. This is the original request in diagram: -g/--genes option to label only the specified regions #248. Mirrors scatter's --gene (singular; -g stays the deprecated --sample-sex alias on diagram, so there is no short form).
• --threshold-low / --threshold-high — directional log2 cutoffs, mutually exclusive with the symmetric -t/--threshold. Label gains at or above --threshold-high and losses at or below --threshold-low; omitting a side suppresses labels in that direction. For example, --threshold-high 0.5 labels gains only, and --threshold-low -25 drops deletion labels while gains still surface.
• Graceful reverse-oriented intervals — intervals stored with start > end (e.g. reverse-direction PCR primers saved that way in the input BED) are now taken to span [min, max] rather than crashing Biopython's chromosome renderer, which asserts 0 <= start <= end <= length.

Output stability

The symmetric threshold maps internally to the directional pair (-t, +t), for which log2 >= high or log2 <= low is exactly abs(log2) >= threshold. Default diagram invocations therefore produce unchanged output; the new behavior is opt-in via the new flags. No .cnr/.cns/.cnn/SEG/VCF formats are touched.

Tests

14 new tests in test/test_plots.py covering symmetric-default equivalence, each directional mode, the -t/directional mutual-exclusion guard, --gene filtering (including whitespace tolerance and co-binned-neighbor dropping), reverse-interval coordinate normalization, and an end-to-end render. An AST-walk plumbing test pins the new kwargs through _cmd_diagram → create_diagram. Full plots suite passes; ruff and mypy clean.

Docs

doc/plots.rst "Reducing cluttered gene labels" documents the new flags.

Fixes #248.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 73.46939% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.73%. Comparing base (34a697e) to head (e2722ee).

Files with missing lines	Patch %	Lines
cnvlib/commands.py	37.50%	8 Missing and 2 partials ⚠️
cnvlib/diagram.py	90.62%	1 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1104      +/-   ##
==========================================
+ Coverage   70.41%   70.73%   +0.32%     
==========================================
  Files          73       73              
  Lines        7907     7946      +39     
  Branches     1400     1405       +5     
==========================================
+ Hits         5568     5621      +53     
+ Misses       1891     1881      -10     
+ Partials      448      444       -4     

Flag	Coverage Δ
unittests	70.73% <73.46%> (+0.32%)	⬆️

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