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Use the supplied chromosome ID for an implicit complement group - #44
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endrebak merged 1 commit intoOct 27, 2026
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I'll have a look. Thanks |
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With
groups=None,complementdocuments thatchrom_len_idsmust describe one chromosome, but creates group 0 regardless of that chromosome's ID. For intervals[10, 20),[30, 40)on chromosome 7 of length 100, it labels the gaps as chromosome 0 and loses the terminal gap[40, 100).Build the implicit group from the supplied chromosome ID and check the documented single-chromosome precondition. Explicit groups and the native kernel are unchanged.
Validation: 46 tests pass on Python 3.12/3.13/3.14 with NumPy 2.5.4, and on 3.12 with NumPy 1.26.4; eight regression cases fail before the change. An independent interval-union reference on public chrX/chrY exon and chromosome-size data reproduces 32 truncated/mislabelled configurations. Sixteen zero-ID controls and all 48 explicit-group controls remain exact. A clean ABI3 wheel repeats the results, and 16 public PyRanges1 operation results per profile stay unchanged. This branch also combines with #43 without changing either fix's complete workload results.