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33 lines
1.6 KiB
Markdown
33 lines
1.6 KiB
Markdown
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# Demultiplexing Functionality in `obingslibrary`
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This package provides tools for **demultiplexing NGS reads** by matching them against known primer pairs and extracting associated barcodes.
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## Core Types
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- `DemultiplexMatch`: Struct holding alignment results for forward/reverse primers, mismatches, barcode coordinates (`BarcodeStart`, `BarcodeEnd`), and metadata (e.g., sample/experiment info via `PCR`). Includes error handling.
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## Key Methods
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- **`Match(sequence)`**:
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Scans the input `BioSequence` against all primer pairs in `NGSLibrary.Markers`. Returns a populated `DemultiplexMatch` if any primer pair matches.
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- **`ExtractBarcode(sequence, inplace)`**:
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Uses the result of `Match()` to:
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- Extract the barcode region (if valid: non-dimer).
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- Reverse-complement if read is in reverse orientation (`IsDirect == false`).
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- Annotate the sequence with:
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- Primer names and match details (positions, mismatches).
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- Direction (`direct`/`reverse`).
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- Sample/experiment info (if assignment succeeds), or error message.
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## Behavior Notes
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- **Primer dimer detection**: If `BarcodeStart > BarcodeEnd`, the read is flagged as a primer dimer and not extracted.
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- **Error handling**: Errors (e.g., no match, sample unassignment) are stored in `match.Error` and propagated as annotations.
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- **Annotation richness**: Output sequences carry rich metadata (sample, experiment, primers, errors), supporting downstream filtering/analysis.
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## Dependencies
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- Uses `logrus` for fatal logging (e.g., subsequence extraction failure).
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- Integrates with `obiseq.BioSequence` for sequence representation and manipulation.
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