Allow G123 to run without phasing analysis when no default phasing exists#963
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SKM2227229725 wants to merge 1 commit intomalariagen:masterfrom
Open
Allow G123 to run without phasing analysis when no default phasing exists#963SKM2227229725 wants to merge 1 commit intomalariagen:masterfrom
SKM2227229725 wants to merge 1 commit intomalariagen:masterfrom
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jonbrenas
requested changes
Mar 8, 2026
| name = "g123_gwss_v1" | ||
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| valid_sites = self.phasing_analysis_ids + ("all", "segregating") | ||
| # Allow None as a valid site (meaning unphased/all sites) |
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I don't think it does what you say. It still uses the _default_phasing_analysis, which is a phasing analysis and thus excludes unphased data.
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@jonbrenas Thanks for the review and for pointing this out. I will re-check the implementation to ensure that G123 can run without relying on |
Author
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Thanks for the review. I will work on the requested changes. Please assign this to me. |
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Fixes #795
Summary
Previously,
g123_gwss()required a default phasing analysis ID,which caused an assertion error for datasets such as
amin1andadir1where no phasing analysis is available.
What this PR changes
sites=Nonewhen no default phasing analysis existsNoneto valid site optionsRationale
G123 uses unphased genotype data for the main calculation.
Requiring a phasing analysis ID should not be mandatory for
datasets that do not provide phasing data.
This change enables G123 to run cleanly on such datasets
without breaking existing behaviour.