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refactor(runall/align): split align+merge into a backend trait and a shared merge - #987
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Included review availability: This review used your included allowance. 1 included review remains after this review. Your included PR review attempts over the past 7 days set your current allowance at 2 reviews per hour. WalkthroughThe alignment path now selects a backend through ChangesAlignment Backend and Merge Pipeline
Priority: ⬇️ Low Estimated code review effort: 4 (Complex) | ~45 minutes Change: Refactor Sequence Diagram(s)sequenceDiagram
participant ChainBuilder
participant SubprocessAlignStep
participant MergeAlignedStep
participant DownstreamPipeline
ChainBuilder->>SubprocessAlignStep: Wire subprocess backend
ChainBuilder->>MergeAlignedStep: Wire shared merge step
SubprocessAlignStep->>MergeAlignedStep: Emit ZipperBatch
MergeAlignedStep->>DownstreamPipeline: Emit ordinal-ordered BamTemplateBatch
Merge Risk: ⚪ Minimal · up to No actionable merge-blocking risk remains from the reviewed alignment changes after normal checks. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #987 +/- ##
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- Coverage 96.17% 96.15% -0.03%
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Files 294 296 +2
Lines 148109 148428 +319
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+ Hits 142438 142715 +277
- Misses 5671 5713 +42 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Review comments at @src/lib/pipeline/steps/align/mod.rs:
- Around line 214-224: Update ZipperBatch::heap_size to include the mapped Vec’s
reserved backing storage, using the existing container_bytes helper if
available, so its accounting matches the unmapped batch. Correct the method
comment to reflect that vector allocation overhead is included.
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📒 Files selected for processing (11)
src/lib/aligner.rssrc/lib/commands/zipper.rssrc/lib/pipeline/chains/builder.rssrc/lib/pipeline/chains/commands/align.rssrc/lib/pipeline/chains/stage.rssrc/lib/pipeline/steps/align/merge.rssrc/lib/pipeline/steps/align/mod.rssrc/lib/pipeline/steps/align/subprocess.rssrc/lib/pipeline/steps/mod.rssrc/lib/pipeline/steps/templates_to_records.rssrc/lib/pipeline/steps/types.rs
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RefillDrainScheduler walks drain-first (downstream-first) like DrainFirstScheduler, except while a step's refill signal is raised: then it walks forward through the steps up to and including a named refill step (so upstream decode can read the next batch ahead) and drain-first over the rest. An optional byte cap on the queue feeding a named step stops the read-ahead once that queue holds enough. The scheduler binds to the run's bounded queues once, when the pipeline is built. WalkDirection gains RefillThenReverse, and the round-robin dispatch maps it to a visit order in one place (walk_position), covered by a case table.
Pure move ahead of splitting the align stage into a backend trait: the file becomes the subprocess backend under a new `steps::align` module. Only the module declaration and the two `align_and_merge::` paths that name it change, so the tree builds unchanged.
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…shared merge The align stage's single Serial AlignAndMergeStep aligned each batch through the aligner subprocess and zipper-merged it on the dispatching worker. It is now an `AlignBackend` trait whose `wire` appends a backend's steps after the queryname-grouped input and returns its merged tail plus the scheduling facts the chain builder folds in (worker floor, drain-first preference). The subprocess backend is the only one: a Serial `SubprocessAlignStep` (the former step, minus the inline merge) emitting `ZipperBatch`es, followed by a Parallel `MergeAlignedStep` that runs the unchanged zipper merge on many batches at once and restores input order from each batch's serial. `ResolvedAligner` now carries a `ResolvedBackend` and `backend_for` builds the backend from it, so the framework-agnostic `aligner` module does not depend on the pipeline's align stage. The @SQ-consistency errors read "@sq count/name/length" (the moved messages had lost the space). Merged output is unchanged.
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Part 2 of 5 of the in-process bwa-mem3 aligner stack (#986 → #987 (this PR) → #988 → #989 → #990).
Summary
Splits
runall's align stage into anAlignBackendtrait and a shared parallel zipper merge, so a second backend can plug in without duplicating the merge. Only the existing subprocess backend exists after this change, and its output is unchanged.align_and_merge.rsmoves toalign/subprocess.rsin its own commit (puregit mvplus path fixups), so the refactor diff is reviewable.AlignBackend::wireappends a backend's steps after the queryname-grouped tail and returns the merged tail plus scheduling hints (AlignWired: minimum workers, drain-first preference); the chain builder folds those into the pool configuration. The subprocess backend keeps today's floor of 4 workers.MergeAlignedStep/merge_zipper_batch(align/merge.rs) hold the zipper merge both backends will share.backend_forbuilds the backend a resolved--aligner::*selection names, soaligner.rs(the framework-agnostic subprocess primitive) no longer depends on the pipeline steps.@SQcount/@SQname/@SQlengthwording in the @SQ-consistency errors to@SQ count/@SQ name/@SQ length.Risk: no output change for any command (only those error message strings); no
unsafe; no memory-bound, queue-capacity or thread-policy change (the subprocess backend's worker floor and queues are carried over as they were).Tests
Existing align/zipper tests move with the code; the scheduling-fold matrix pins the backends' real hints (
SubprocessBackend::MIN_WORKERS/PREFERS_DRAIN_FIRST) rather than literals.Risk: Output—no intended changes beyond corrected
@SQerror wording; header and merge tests cover key cases, but no runtime test results are supplied. Unsafe—none added; no CLAUDE.md allowlist update is indicated. Resource policy—the subprocess byte budget is derived from chunk size, and its four-worker minimum and drain-first preference feed pool scheduling.The align stage now uses an
AlignBackendtrait, with a subprocess backend and a shared parallel zipper merge. The merge preserves batch order and rejects mismatched mapped and unmapped template counts. The chain builder skips queryname grouping when its input is already grouped, then folds backend scheduling hints into the pool configuration.