obitools4/autodoc/docmd/pkg/obingslibrary/ngslibrary.md

Semantic Description of obingslibrary Package

The obingslibrary package defines core data structures and methods for managing PCR-based NGS library designs, particularly in metabarcoding workflows.

• PrimerPair and TagPair: Represent forward/reverse primer or tag sequences.
• PCR: Encapsulates a single PCR amplification experiment with sample metadata and annotations (via obiseq.Annotation).
• NGSLibrary: Central struct storing primer definitions (Primers) and associated marker specifications (Markers), where each Marker defines how primers (and attached tags) are processed.

Key functionality includes:

• Dynamic marker creation: GetMarker() lazily initializes a new Marker for any primer pair if not already present.
• Compilation: Two compilation modes (Compile, Compile2) prepare internal search structures (e.g., error-tolerant index) using user-defined parameters like max errors and indel allowance.
• Tag configuration: Methods to set spacer length, delimiter character (e.g., N or X), and indel tolerance for tags—globally (SetTagSpacer, etc.) or per-primer.
• Matching strategy: Configure alignment behavior (e.g., "strict" vs. "fuzzy") via SetMatching*.
• Unicity & validation: CheckPrimerUnicity() ensures no primer is reused across multiple markers and prevents self-complementary pairs.
• Error handling: Supports configurable mismatch/indel budgets per primer direction.

This library enables flexible, reproducible specification of molecular identifiers (tags) and amplification primers—essential for accurate demultiplexing and sequence assignment in high-throughput sequencing pipelines.