fix(import-rna): wire --diploid-parx-genome and make it effective

[etal]

Summary

The import-rna command accepted no --diploid-parx-genome flag, so the pseudo-autosomal-region-aware re-centering already implemented in do_import_rna was unreachable from the command line. This change registers the shared flag on the import-rna parser and forwards args.diploid_parx_genome into the do_import_rna call.

Wiring the flag alone is insufficient. cnvlib/rna.py:correct_cnr applies GC- and transcript-length window correction (enabled by default), which is invariant to a uniform pre-shift of the log2 values. The first center_all(diploid_parx_genome=...) only changes a global centering constant; that contribution is absorbed by the window correction and then overwritten by a second, unconditional center_all() that omitted the flag. As a result, the flag changed output only under --no-gc --no-txlen. The second center_all now also carries diploid_parx_genome, so PAR-aware centering takes effect on the default path.

Clinical impact

Enabling --diploid-parx-genome changes chromosome-X / PAR log2 output for the named genome (e.g. grch38). The default path — flag omitted, diploid_parx_genome=None — is bit-exact with prior output, since center_all(None) resolves to autosomes(None) exactly as before. No change to .cnr output for existing default invocations.

Tests

• DiploidParxPlumbingTests — AST-level guards that _cmd_import_rna forwards diploid_parx_genome to do_import_rna, that the CLI registers --diploid-parx-genome, and that the signature default is None. These fail at collection if the kwarg is dropped, at no fixture cost.
• DiploidParxCenteringTests — behavior tests on an hg38-style fixture: the flag shifts PAR centering under the default GC/txlen corrections (guarding the second-center_all fix), and is inert when no PAR bins are present (confirming it touches only PAR-X).

Full suite: 457 passed. ruff and mypy clean.

Docs

New "Pseudo-autosomal regions on chromosome X" subsection in doc/rna.rst.

Closes cnvkit-d68.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 70.76%. Comparing base (849a32b) to head (ff4edf6).

Additional details and impacted files

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  Coverage   70.75%   70.76%           
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  Files          73       73           
  Lines        7951     7952    +1     
  Branches     1407     1407           
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+ Hits         5626     5627    +1     
  Misses       1881     1881           
  Partials      444      444           

Flag	Coverage Δ
unittests	70.76% <100.00%> (+<0.01%)	⬆️

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