chore(bam): remove two dead pipeline completion flags

[nh13]

Follow-up to #656, found while auditing BamPipelineState's completion graph. Independent of that PR — this branches from main and touches none of the same lines.

Two *_done flags were dead:

Flag	State
decompress_done	Declared and initialized, then never touched — never set, never read.
decode_done	Set in exactly one place, read nowhere. Write-only state that looked load-bearing.

Neither is missed

• Decompress is tracked downstream through batches_decompressed, and FindBoundaries infers its completion from batches_boundary_processed == next_read_serial — nothing can be processed that was not decompressed first.
• Decode is tracked by Group through batches_grouped == batches_boundary_found.

Both are recorded as comments where the fields were, so the next reader doesn't go looking for a flag that was deliberately removed.

Why decode_done is worth deleting rather than leaving

Its guard was boundary_done && q2b_boundaries.is_empty(), which does not account for a batch sitting in a worker's held_boundaries. Anyone who wired the flag up to a consumer would have reintroduced exactly the stranded-batch bug #656 fixes in FindBoundaries — the flag is inert today only by accident. Deleting it removes the trap instead of leaving a loaded gun behind a plausible-looking name.

Behavior

Unchanged. Dropping the store left the else if arm that records Q2b starvation as the only live branch, so the two state.stats() blocks fold into one. The recording condition is the De Morgan equivalent of the original (!(boundary_done && q2b empty)), and the comment now explains why an empty Q2b past that point is the terminal state rather than a stall.

Both fields were pub on BamPipelineState — internal pipeline machinery with no reader outside the module.

cargo ci-test (6586 tests), ci-fmt, ci-lint, and ci-doc all pass.

Coverage

Rewriting that stats arm dropped patch coverage to 0% on the three lines it touches — state.stats() is None unless stats collection is enabled, and nothing turned it on, so the arm had never been exercised. It is covered now by test_decode_records_q2_starvation_only_while_boundaries_may_arrive, which also turns the "condition unchanged" claim above into something checked rather than asserted: inverting the condition fails both cases.

Summary by CodeRabbit

• Bug Fixes
  • Improved BAM processing completion and queue-handling behavior.
  • Reduced incorrect starvation reporting when no additional boundaries can arrive.
  • Improved pipeline end-of-step detection using batch and boundary progress.

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Reviewing files that changed from the base of the PR and between 0f97f40 and da5d018.

📒 Files selected for processing (1)

• src/lib/unified_pipeline/bam.rs

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Walkthrough

BAM pipeline completion tracking now relies on decompressed/grouped counters and boundary state instead of explicit flags. Decode starvation accounting and its test cases were updated for empty Q2b queues and boundary arrival conditions.

Changes

BAM completion tracking

Layer / File(s)	Summary
Counter-based completion state src/lib/unified_pipeline/bam.rs	Removes decompress_done and decode_done from BamPipelineState and its constructor, documenting counter-based completion semantics.
Boundary-aware decode termination src/lib/unified_pipeline/bam.rs	Updates decode starvation accounting to use boundary_done and q2b_boundaries, and revises tests for the resulting behavior.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• fulcrumgenomics/fgumi#656: Changes how boundary_done is set, which directly affects the updated decode completion semantics.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the main change: removing two unused BAM pipeline completion flags.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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• Commit unit tests in branch nh/chore-remove-dead-pipeline-done-flags

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.65%. Comparing base (0f97f40) to head (da5d018).
⚠️ Report is 5 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #657   +/-   ##
=======================================
  Coverage   93.64%   93.65%           
=======================================
  Files         175      175           
  Lines      107492   107487    -5     
=======================================
- Hits       100664   100662    -2     
+ Misses       6828     6825    -3     

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[nh13]

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