staar: ld-prune subcommand for LD pruning on conditional p-values#129
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staar: ld-prune subcommand for LD pruning on conditional p-values#129
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Forward selection over a candidate variant list using score-test p-values conditional on the growing known-loci set, mirroring STAARpipeline R/LD_pruning.R:146-185. Each iteration refits the null via augment_covariates at src/staar/pipeline.rs:581-588, rescores remaining candidates under the refit null, and stops when the best conditional p falls above --cond-p-thresh. Single-trait gaussian unrelated path only; binary and kinship-aware nulls reject at callsite. Adds src/staar/ld_prune.rs (core loop, four unit tests over synthetic carrier lists covering trivial, collinear, orthogonal, and empty cases) and src/commands/ld_prune.rs (CLI surface, candidates-file parser for tab or colon delimited rows, TSV output).
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Forward-selection LD pruning over a candidate variant list using score-test p-values conditional on the growing known-loci set. Follows STAARpipeline R/LD_pruning.R:146-185. Each iteration refits the null via augment_covariates, rescores the remaining candidates under the refit, and stops when the best conditional p falls above --cond-p-thresh.
Single-trait gaussian unrelated path only. Binary and kinship-aware nulls are out of scope here; those land with the broader kinship-in-conditional work.
src/staar/ld_prune.rs holds the core loop and four unit tests (trivial, perfectly collinear partner drops out, orthogonal signals both survive, empty input). src/commands/ld_prune.rs wires the CLI surface, parses the candidates file (tab- or colon-delimited CHR POS REF ALT), and writes a TSV with an entry_log10p column recording the p-value at which each variant entered the pruned set.
Closes #103.