obitools4/autodoc/docmd/pkg/obitools/obimultiplex/demultiplex.md

obimultiplex.IExtractBarcode — Semantic Description

The function IExtractBarcode performs demultiplexing of high-throughput sequencing data by extracting and assigning molecular barcodes (e.g., sample indices) to biological sequences.

• Input: An iterator over BioSequence objects (obiiter.IBioSequence) representing raw sequencing reads.

• Core Logic: Uses the obingslibrary package to configure and instantiate a multi-barcode extraction worker.

• Configuration Options:

  • AllowedMismatches: Tolerates up to N mismatches in barcode matching (via CLIAllowedMismatch()).
  • AllowedIndel: Permits insertions/deletions in barcode alignment (via CLIAllowsIndel()).
  • Unidentified: If specified, writes unassigned reads to a file (via CLIUnidentifiedFileName()).
  • DiscardErrors: Controls whether reads failing barcode matching are retained or filtered (via CLIConservedErrors()).
  • Parallelization: Uses configurable worker threads and batch sizes (from obidefault).

• Processing Flow:

  • Applies barcode extraction via .MakeISliceWorker(...), enabling parallel processing.
  • If error conservation is disabled, filters out sequences with the "obimultiplex_error" attribute (i.e., unassigned reads).
  • Optionally spawns a goroutine to persist unidentified sequences to disk using obiconvert.CLIWriteBioSequences.

• Output: Returns an iterator over assigned and barcode-extracted sequences, ready for downstream analysis (e.g., merging with primers or taxonomic assignment).

• Logging: Provides runtime feedback on worker count, discarded/retained behavior, and output file usage.

This function implements robust, configurable demultiplexing suitable for large-scale NGS pipelines.