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feat(pipeline): add the typed-step pipeline tree with its foundational steps (R1a) - #735

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nh13 merged 2 commits into
main-runallfrom
nh/runall-11-pipeline-steps
Aug 12, 2026
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feat(pipeline): add the typed-step pipeline tree with its foundational steps (R1a)#735
nh13 merged 2 commits into
main-runallfrom
nh/runall-11-pipeline-steps

feat(pipeline): add the typed-step pipeline tree with its foundationa…

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Codecov Report

❌ Patch coverage is 92.43499% with 128 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (main-runall@01284b2). Learn more about missing BASE report.

Files with missing lines Patch % Lines
src/lib/pipeline/steps/parse/bam.rs 85.30% 31 Missing ⚠️
src/lib/pipeline/steps/boundaries/state.rs 92.37% 28 Missing ⚠️
src/lib/pipeline/steps/parse/decode.rs 90.52% 27 Missing ⚠️
src/lib/pipeline/steps/boundaries/bam.rs 87.50% 10 Missing ⚠️
src/lib/pipeline/steps/bgzf/decompress.rs 86.76% 9 Missing ⚠️
src/lib/pipeline/steps/parse/sam.rs 96.40% 9 Missing ⚠️
src/lib/pipeline/steps/bgzf/compress.rs 94.77% 8 Missing ⚠️
src/lib/template.rs 88.23% 4 Missing ⚠️
src/lib/pipeline/steps/types.rs 98.84% 2 Missing ⚠️
Additional details and impacted files 
@@              Coverage Diff               @@
##             main-runall     #735   +/-   ##
==============================================
  Coverage               ?   93.96%           
==============================================
  Files                  ?      241           
  Lines                  ?   128338           
  Branches               ?        0           
==============================================
  Hits                   ?   120598           
  Misses                 ?     7740           
  Partials               ?        0

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