Add multi-threading control for colocboost pipeline #429
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- Check for missing phenotype, covariate, genotype, sumstat, column mapping, and LD metadata files - Error (not warn) when files are missing to catch path issues early - Fix genotype file check to look for .bed/.bim/.fam or .pgen/.pvar/.psam files instead of base filename - Improve error messages to show which files are missing with condition names - Filter phenotypes without data for specific region before loading
- Centralize normalize_variant_id function in misc.R and remove duplicates - Normalize variant IDs consistently across sumstats, LD matrices, and genotype data - Fix LD matrix usage: use processed LD matrices after normalization in summary_stats_qc - Normalize ref_panel variant IDs before imputation to match processed sumstats - Add try-catch error handling in summary_stats_qc_multitask loop - Add try-catch error handling in separate_gwas focal analysis loop - Fix pip_cutoff_to_skip_sumstat handling for single values, named vectors, and unnamed vectors - Remove debug statements
…alyses - Use normalize_variant_id() consistently for sumstats and LD matrices to handle variant ID format mismatches - Remove double 'chr' prefix issue and build suffix (e.g., :b38) mismatches - Add tryCatch error handling for joint_gwas and separate_gwas analyses - Add concise warning messages for colocboost validation failures - Fix sumstat_studies handling when sumstats list is empty
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Summary
Add
num_threadsparameter to control parallel processing in colocboost data loading.Changes
num_threadsparameter to colocboost pipelineload_multitask_regional_datafunctionRationale
Enables better control of computational resources for HPC environments.