mirror of https://github.com/metabarcoding/obitools4.git synced 2026-04-30 12:00:39 +00:00

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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

PCR Simulation and Barcode Extraction Module

This Go package (obingslibrary) provides configuration-driven tools for PCR simulation and barcode extraction from NGS libraries.

Core Concepts

Options: A fluent configuration object for customizing behavior via functional setters.
Default options are defined in MakeOptions, supporting:
- Error handling (discardErrors)
- Mismatch/indel tolerance via allowedMismatch and allowsIndel
- Parallelization (parallelWorkers) and batching control (batchSize)
- Optional progress tracking (withProgressBar)

Barcode Extraction:
- ExtractBarcodeSlice: Extracts barcodes from a slice of sequences using the NGS library, applying configured error handling and alignment parameters.
- ExtractBarcodeSliceWorker: Returns a reusable worker function for batch processing (e.g., in pipelines or parallel workers).
Compilation Step:
- ngslibrary.Compile(...) prepares internal indexing based on mismatch/indel settings before extraction.
Error Handling:
- If discardErrors is true (default), sequences causing extraction errors are filtered out.
- Alternatively, error-containing reads can be retained or logged via OptionUnidentified.

Uses the option pattern for extensibility and clean API.
Integrates with default settings from obidefault (e.g., parallelism, batch size).
Designed for both direct use and integration into concurrent workflows.