mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
18 lines
1.7 KiB
Markdown
18 lines
1.7 KiB
Markdown
# 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.
|