obitools4/autodoc/docmd/pkg/obiapat/pcr.md

PCR Simulation Module (obiapat)

This Go package implements a PCR (Polymerase Chain Reaction) simulation algorithm for biological sequence analysis. It supports flexible primer matching, amplicon extraction with optional flanking extensions, and handles both linear and circular DNA topologies.

Key Functionalities

• Primer Matching: Accepts forward/reverse primers with configurable mismatch tolerance (OptionForwardPrimer, OptionReversePrimer). Internally builds pattern objects and their reverse complements.
• Amplicon Extraction: Identifies valid amplicons bounded by primer pairs, respecting user-defined length constraints (OptionMinLength, OptionMaxLength).
• Extension Support: Optionally adds fixed-length flanking regions (OptionWithExtension) — either strict full-extension only or partial trimming allowed.
• Topology Handling: Supports linear (Circular: false) and circular DNA sequences via OptionCircular.
• Batch & Parallel Processing: Configurable batch size (OptionBatchSize) and parallel workers count (OptionParallelWorkers), enabling efficient processing of large datasets.
• Annotation-Rich Output: Each amplicon includes detailed annotations (primer sequences, match positions, errors, direction), preserving original sequence metadata.

Core API

• PCRSim(sequence, options...): Simulates PCR on a single sequence.
• PCRSlice(sequencesSlice, options...): Applies simulation across multiple sequences in a slice.
• PCRSliceWorker(options...): Returns a reusable worker function for parallel execution via obiseq.MakeISliceWorker.

Implementation Details

• Uses pattern-matching (ApatPattern) with fuzzy search to locate primers.
• Handles circular topology by wrapping indices around sequence boundaries.
• Reuses internal memory via MakeApatSequence/Free, supporting efficient GC and large-scale processing.
• Logs critical errors with logrus; debug-level details for amplicon generation.

Designed to integrate within the OBITools4 ecosystem, this module enables high-fidelity in silico PCR for metabarcoding and NGS data validation workflows.