obitools4/autodoc/docmd/pkg/obichunk/chunk.md

ISequenceChunk Function — Semantic Description

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.

• It accepts an iterator over biological sequences (obiiter.IBioSequence) and a sequence classifier (obiseq.BioSequenceClassifier), used to annotate or categorize sequences.
• A boolean flag onMemory determines whether processing occurs in RAM (ISequenceChunkOnMemory) or on disk (ISequenceChunkOnDisk), enabling scalability for large datasets.
• Optional parameters allow fine-tuning:
  • dereplicate: enables deduplication of identical sequences.
  • na: specifies how missing or ambiguous values are handled (e.g., "?", "N", etc.).
  • statsOn: configures what metadata (e.g., description fields) are tracked for statistics.
  • uniqueClassifier: an optional secondary classifier used to assign unique identifiers or labels.

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.

This design promotes flexibility, memory efficiency, and modularity in high-throughput sequence analysis pipelines (e.g., metabarcoding).