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

Demultiplexing Functionality in `obingslibrary`

This package provides tools for demultiplexing NGS reads by matching them against known primer pairs and extracting associated barcodes.

Core Types

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.

Match(sequence):
Scans the input BioSequence against all primer pairs in NGSLibrary.Markers. Returns a populated DemultiplexMatch if any primer pair matches.
ExtractBarcode(sequence, inplace):
Uses the result of Match() to:
- Extract the barcode region (if valid: non-dimer).
- Reverse-complement if read is in reverse orientation (IsDirect == false).
- Annotate the sequence with:
  - Primer names and match details (positions, mismatches).
  - Direction (direct/reverse).
  - Sample/experiment info (if assignment succeeds), or error message.

Primer dimer detection: If BarcodeStart > BarcodeEnd, the read is flagged as a primer dimer and not extracted.
Error handling: Errors (e.g., no match, sample unassignment) are stored in match.Error and propagated as annotations.
Annotation richness: Output sequences carry rich metadata (sample, experiment, primers, errors), supporting downstream filtering/analysis.

Uses logrus for fatal logging (e.g., subsequence extraction failure).
Integrates with obiseq.BioSequence for sequence representation and manipulation.