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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)
16 lines
1.4 KiB
Markdown
16 lines
1.4 KiB
Markdown
# `ISequenceChunk` Function — Semantic Description
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The `ISequenceChunk` function provides a unified interface for processing biological sequence data in chunks, supporting two execution modes: **in-memory** and **on-disk**, depending on resource constraints or performance needs.
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- It accepts an iterator over biological sequences (`obiiter.IBioSequence`) and a sequence classifier (`obiseq.BioSequenceClassifier`), used to annotate or categorize sequences.
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- A boolean flag `onMemory` determines whether processing occurs in RAM (`ISequenceChunkOnMemory`) or on disk (`ISequenceChunkOnDisk`), enabling scalability for large datasets.
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- Optional parameters allow fine-tuning:
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- `dereplicate`: enables deduplication of identical sequences.
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- `na`: specifies how missing or ambiguous values are handled (e.g., `"?"`, `"N"`, etc.).
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- `statsOn`: configures what metadata (e.g., description fields) are tracked for statistics.
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- `uniqueClassifier`: an optional secondary classifier used to assign unique identifiers or labels.
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The function abstracts the underlying implementation, ensuring consistent behavior regardless of storage strategy. It returns an iterator over processed sequences (`obiiter.IBioSequence`) or an error, supporting streaming workflows and compatibility with downstream pipeline stages.
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This design promotes flexibility, memory efficiency, and modularity in high-throughput sequence analysis pipelines (e.g., metabarcoding).
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