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adding phased property to HaplotypeMatrix - #354
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🟡 Changes recommended
The streaming constructor breaks existing callers by requiring a new argument, and the quickstart contains inaccuracies about VCF ploidy, haplotype values, and dosage conversion.
4 open issues
What changed in this PR
Adds informational phasing metadata to eager and streaming haplotype matrices, preparing the codebase for future phase-aware warnings without changing statistical results.
Changes:
- Adds
phasedandset_phased(), with loader-specific defaults. - Preserves phasing through subsets, filtering, streaming chunks, and windowed matrices.
- Adds tests, updates documentation, and outlines future warning behavior.
| File | Description |
|---|---|
| tests/test_streaming.py | Supplies phasing explicitly in streaming construction. |
| tests/test_phasing.py | Tests defaults, overrides, propagation, and conversions. |
| tests/test_gpu_genotype_prep.py | Updates builder calls with explicit phasing. |
| PHASING_PLAN.md | Outlines future phase-dependent warnings and follow-ups. |
| pg_gpu/windowed_analysis.py | Preserves phasing in per-window matrices. |
| pg_gpu/streaming_matrix.py | Adds streaming phasing metadata and chunk propagation. |
| pg_gpu/haplotype_matrix.py | Adds the flag, loader defaults, and propagation. |
| pg_gpu/genotype_matrix.py | Marks reconstructed haplotypes as unphased. |
| pg_gpu/_utils.py | Preserves phasing in population subsets. |
| pg_gpu/_gpu_genotype_prep.py | Requires and forwards explicit phasing. |
| docs/source/quickstart.rst | Explains phasing flags and matrix conversions. |
| docs/source/changelog.rst | Announces informational phasing support. |
| docs/source/api.rst | Exposes streaming phasing members in API documentation. |
Review effort: Balanced
| """ | ||
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| def __init__(self, source, fetcher, chunk_bp, prefetch, *, | ||
| phased, accessible_mask=None, n_total_sites=None): |
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| per haplotype, with variants as columns). When loaded from a diploid | ||
| (or n-ploid) VCF, the two haploid copies of each sample become 2 (or n) rows. |
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| ``HaplotypeMatrix`` rows are gametes (0/1 per allele, two rows per | ||
| individual). ``GenotypeMatrix`` rows are individuals (0/1/2 dosage). |
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| # Convert from haploid (pairs consecutive haplotypes). | ||
| # The result is always phased=False: heterozygotes are assigned as | ||
| # (0, 1), which is a pseudo-phasing. |
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| (0/1/2 dosage). Use ``GenotypeMatrix`` only for statistics which need | ||
| dosage encoding. Many functions auto-dispatch on input type, so the same | ||
| call works on either a ``HaplotypeMatrix`` or a ``GenotypeMatrix``. |
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WIP