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feat(runall/inproc): align in process with bwa-mem3 (--aligner::preset bwa-mem3-inproc) - #990

Merged
nh13 merged 3 commits into
mainfrom
nh/inproc-aligner
Sep 30, 2026
Merged

nh13 merged 3 commits into
mainfrom
nh/inproc-aligner

feat(runall/inproc): skip seeding duplicate read pairs (--aligner::de…

16f62fb
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Codecov / codecov/project succeeded Sep 30, 2026 in 0s

96.31% (-0.02%) compared to bc7f67e

View this Pull Request on Codecov

96.31% (-0.02%) compared to bc7f67e

Details

Codecov Report

❌ Patch coverage is 92.95154% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.31%. Comparing base (bc7f67e) to head (16f62fb).

Files with missing lines Patch % Lines
src/lib/pipeline/chains/builder.rs 76.47% 8 Missing ⚠️
src/lib/aligner.rs 95.95% 7 Missing ⚠️
src/lib/pipeline/steps/align/mod.rs 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #990      +/-   ##
==========================================
- Coverage   96.33%   96.31%   -0.02%     
==========================================
  Files         298      298              
  Lines      149522   149706     +184     
==========================================
+ Hits       144040   144191     +151     
- Misses       5482     5515      +33     

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