staar: _cond suffix on conditional output files#128
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The conditional math already runs today — augment_covariates at pipeline.rs:581-588 expands X with known_loci before the null is fit, and by the OLS projection identity that is mathematically equivalent to R's method_cond="optimal" two-stage procedure (regress y~X, then residuals on [known_loci, X]). Downstream score tests see the Schur-complement- projected K = G'(I - H_aug)G automatically. What was missing: the output files didn't say so. This PR suffixes mask-level outputs with _cond and sets meta.conditional=true when --known-loci is active, matching STAARpipelineSummary's file layout (coding_plof.parquet vs coding_plof_cond.parquet) so the summary tooling can tell conditional from unconditional runs. SPA + --known-loci now emits a warning: SPA reads raw G not the augmented projection, so gene-mask p-values in that combo are SPA- adjusted but not conditional. The cond-SPA variant (Gene_Centric_*_cond_spa in R) is a follow-up. 296/296, clippy clean.
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Closes #102.
The conditional math already runs today: augment_covariates at pipeline.rs:581-588 expands X with --known-loci before the null is fit, and by the OLS projection identity that is mathematically equivalent to R's method_cond="optimal" two-stage procedure. Downstream score tests see K = G'(I - H_aug)G automatically.
Gap was output: filenames didn't say so. This suffixes mask outputs with _cond and sets meta.conditional=true when --known-loci is active, matching STAARpipelineSummary's layout so summary tooling can tell conditional from unconditional runs.
SPA + --known-loci now warns: SPA reads raw G not the augmented projection, so gene-mask p-values are SPA-adjusted but not conditional. The cond-SPA variant (Gene_Centric_*_cond_spa in R) is a follow-up.
296/296, clippy clean.