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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
30 lines
2.0 KiB
Markdown
30 lines
2.0 KiB
Markdown
# Semantic Description of `obichunk.ISequenceSubChunk`
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The function `ISequenceSubChunk` in the `obichunk` package implements **parallel, class-based sorting and batching of biological sequences**, preserving input order within each batch while reordering across batches by classification code.
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## Core Functionality
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- **Input**:
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- An iterator over `BioSequence` batches (`obiiter.IBioSequence`)
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- A sequence classifier (`obiseq.BioSequenceClassifier`) assigning each sequence a numeric class code
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- A number of worker goroutines (`nworkers`), defaulting to system-configured parallelism
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- **Processing**:
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- Each worker consumes its own iterator split and classifier clone, enabling concurrent batch processing.
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- For each incoming `BioSequenceBatch`:
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- If the batch has >1 sequence: sequences are extracted, classified into `code`, and sorted *in-place* by class code.
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- Consecutive sequences with the same `code` are grouped into new batches; a new batch is emitted upon code change.
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- If the batch has ≤1 sequence, it’s passed through unchanged (but reordered with a new order ID).
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- **Ordering Mechanism**:
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- Uses `atomic.AddInt32` to assign strictly increasing order IDs (`nextOrder`) across workers, preserving deterministic inter-batch ordering.
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- Sorting within batches is performed via a custom `sort.Interface` implementation using closures for flexible comparison logic (here, by ascending class code).
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- **Output**:
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- Returns a new iterator (`obiiter.IBioSequence`) emitting batches grouped by classification code, with globally ordered batch IDs.
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- Workers are coordinated via `newIter.Done()`/`Wait()/Close()`, ensuring clean termination.
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## Semantic Purpose
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Enables efficient, parallel **grouping of sequences by taxonomic or functional class** (e.g., OTU assignment), optimizing downstream processing that requires sorted/class-ordered input — e.g., consensus building, alignment, or read merging per group.
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