simple fix - removing colocboost::#503
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ColocBoost adapters now accept genotype-backed LDData objects from load_LD_matrix(), preserving X_ref-based paths instead of treating LDData as a legacy list. Added regression coverage for direct RegionalData conversion, direct ColocBoost QC input prep, and summary-stat QC with S4 LDData.
Bug: long transMap and ColocBoost runs could appear to hang at the last visible pipeline handoff step because .run_colocboost emitted no message before entering colocboost_analysis(). This made slow ColocBoost calls look like upstream LD argument construction or handoff failures. Fix: emit a start message immediately before colocboost_analysis(), capture the elapsed difftime once, emit an exit timing message after the call returns, and keep the existing result/time return contract unchanged.
Change the internal ColocBoost dispatch from colocboost::colocboost to the unqualified colocboost function, matching the local source-based workflow where colocboost is expected to be available in the runtime environment. Only R/colocboost_pipeline.R is changed.
Update colocboost_analysis documentation to match the unqualified colocboost dispatch. The roxygen comments and generated Rd now refer to colocboost() instead of colocboost::colocboost().
Revert .run_colocboost to its original tryCatch-plus-timing implementation by removing the start and elapsed boundary messages. This keeps the unqualified colocboost dispatch and documentation changes intact.
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I think we also need to update the |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #503 +/- ##
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Coverage 86.26% 86.26%
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Files 52 52
Lines 11642 11642
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Hits 10043 10043
Misses 1599 1599 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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