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coloc, refactor and raiss fixes - #576

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danielnachun merged 6 commits into
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coloc_raiss
Aug 25, 2026
Merged

danielnachun merged 6 commits into
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coloc_raiss

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codecov Bot commented Aug 23, 2026 •

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Codecov Report

❌ Patch coverage is 95.91415% with 158 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.31%. Comparing base (dd7794c) to head (5e53888).
⚠️ Report is 2 commits behind head on main.

Files with missing lines Patch % Lines
R/fineMappingRow.R 95.53% 29 Missing ⚠️
R/ctwasPipeline.R 89.26% 19 Missing ⚠️
R/ColocBoostResult.R 95.37% 13 Missing ⚠️
R/QtlDataset.R 94.91% 12 Missing ⚠️
R/ld.R 93.71% 11 Missing ⚠️
R/fineMappingWrappers.R 89.77% 9 Missing ⚠️
R/AllClasses.R 94.07% 8 Missing ⚠️
R/ColocResult.R 96.17% 8 Missing ⚠️
R/genotypeIo.R 90.36% 8 Missing ⚠️
R/tupleSelectors.R 96.03% 8 Missing ⚠️
... and 11 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #576      +/-   ##
==========================================
- Coverage   97.73%   97.31%   -0.42%     
==========================================
  Files          66       68       +2     
  Lines       25433    27711    +2278     
==========================================
+ Hits        24857    26968    +2111     
- Misses        576      743     +167     

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@danielnachun
danielnachun merged commit 5342a84 into main Aug 25, 2026
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@danielnachun
danielnachun deleted the coloc_raiss branch August 25, 2026 09:08
danielnachun pushed a commit to Yining97/pecotmr that referenced this pull request Aug 30, 2026
Some panels (ADSP R5) name ~3% of variants with a tag where an allele belongs (chr21:...:INS:T), so the id no longer encodes its alleles though A1/A2 are correct. Harmonization keys on the allele columns and keeps the variant; the id-string LD lookup then can't find it and aborts (.fmLdFromSketch / kriging: 'N variant id(s) not present'). The sumstats can't say which orientation was measured at such a position, so drop is the only safe choice -- the same rule StatFunGen#576's RAISS flip-pair/flip-of-known masks apply. Exclude uninterpretable-id panel entries from harmonization (.refVariantsFromSketch, so removeUnmatched drops the variant) and from RAISS (.raissUnsafeToImpute third clause), keyed on a new .ldSketchIdUsable predicate (parses to non-DNA allele; rsIDs and real indels unaffected).
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