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32 lines
1.5 KiB
Markdown
32 lines
1.5 KiB
Markdown
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# PCR Simulation and Barcode Extraction Module
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This Go package (`obingslibrary`) provides configuration-driven tools for **PCR simulation and barcode extraction** from NGS libraries.
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## Core Concepts
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- `Options`: A fluent configuration object for customizing behavior via functional setters.
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- Default options are defined in `MakeOptions`, supporting:
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- Error handling (`discardErrors`)
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- Mismatch/indel tolerance via `allowedMismatch` and `allowsIndel`
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- Parallelization (`parallelWorkers`) and batching control (`batchSize`)
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- Optional progress tracking (`withProgressBar`)
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## Key Functionalities
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- **Barcode Extraction**:
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- `ExtractBarcodeSlice`: Extracts barcodes from a slice of sequences using the NGS library, applying configured error handling and alignment parameters.
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- `ExtractBarcodeSliceWorker`: Returns a reusable worker function for batch processing (e.g., in pipelines or parallel workers).
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- **Compilation Step**:
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- `ngslibrary.Compile(...)` prepares internal indexing based on mismatch/indel settings before extraction.
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- **Error Handling**:
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- If `discardErrors` is true (default), sequences causing extraction errors are filtered out.
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- Alternatively, error-containing reads can be retained or logged via `OptionUnidentified`.
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## Design Highlights
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- Uses the *option pattern* for extensibility and clean API.
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- Integrates with default settings from `obidefault` (e.g., parallelism, batch size).
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- Designed for both direct use and integration into concurrent workflows.
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