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Feat/filter empty phenotypes by region #427

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@kal26 kal26 commented Dec 5, 2025 •
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This PR adds comprehensive file existence checks for all input files and improves error handling.

Changes

  • File existence checks: Added checks for all file types (phenotype, covariate, genotype, sumstat, column mapping, and LD metadata files)
  • Error instead of warnings: Changed from warnings to errors when files are missing to catch path issues early
  • Fixed genotype file check: Now properly checks for .bed/.bim/.fam or .pgen/.pvar/.psam files instead of the base filename
  • Better error messages: Error messages now clearly show which files are missing along with their associated condition/study names
  • Region-based filtering: Filter out phenotypes without data for specific regions before attempting loading

Benefits

  • Catches file path errors immediately instead of failing later
  • Clear error messages make it easy to identify which files are missing
  • Prevents silent failures when files don't exist

kal26 and others added 17 commits October 2, 2025 11:24
@kal26
clean NAs before mutated in alelle_qc
00f2058
@kal26
clean build from LD varaint ids
756b657
@kal26
add missing defualt for pip_cutoff_to_skip_ld
308487e
@kal26
chr anming for LD columns
77630df
@kal26
chr naming for LD columns
50e8dcb
@kal26
chr and build naming in LD variant ids
84e2e51
@kal26
harmonize LD block variants, handel nas in printing
089383f
@kal26
harmonize all to have chr prefix
1b90a95
@kal26
remove nas from sumstats
51ba8e8
@kal26
skip gwas in focal mode if colocboost errors
a2aa4e2
@kal26
Update documentation
e194bad
@kal26
add rss_qc as default qc_method
47ae7d0
@kal26
add default pip_cutoff for multiple individual contexts or sumstats
4d60845
@kal26
get names from region_name_col even if extract_region_name isn't prov…
705eae4 
…ided. Add fallback region nameing (reigon_1, region_2, ..)
@kal26
Merge remote-tracking branch 'origin/set-defaults' into test/all-prs
5d6b91e
@kal26
Merge PRs into test/all-prs
8ec81e4
@kal26
Add comprehensive file existence checks with clear error messages
922e236 
- 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
@kal26 kal26 force-pushed the feat/filter-empty-phenotypes-by-region branch from b6bb933 to 922e236 Compare December 19, 2025 22:04
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