⬆️ 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)

autodoc/docmd/pkg_obitools_obicleandb.md

@@ -0,0 +1,54 @@
+# `obicleandb` Package Overview
+
+The `obicleandb` package delivers semantic curation and trust scoring for biological sequences (e.g., DNA barcodes) within the OBITools4 ecosystem. It combines taxonomic consistency checks, alignment-based discrimination tests, and statistical confidence estimation to ensure high-fidelity sequence datasets for downstream analysis.
+
+## Core Functionalities
+
+### 1. **Input & Taxonomy Integration**
+- Loads reference taxonomies (e.g., NCBI) via `obioptions.LoadTaxonomyOptionSet`.
+- Parses heterogeneous inputs (FASTA/FASTQ) using `obiconvert.InputOptionSet`, supporting streaming and format auto-detection.
+- Integrates taxonomic lineage information into sequence metadata for downstream filtering.
+
+### 2. **Taxonomy-Guided Dereplication & Filtering**
+- `ICleanDB` orchestrates a pipeline that first filters sequences by required taxonomic ranks (e.g., species, genus).
+- Dereplicates identical sequences *within* taxonomic groups (e.g., collapse duplicates per `taxid`), preserving only one representative per unique sequence–taxon pair.
+- Ensures minimal taxonomic resolution before scoring (e.g., requires at least genus-level assignment).
+
+### 3. **Sequence Trust Scoring**
+- `SequenceTrust`: Computes *local* confidence as  
+  \[
+    s = 1 - \frac{1}{n + 1}
+  \]  
+  where `n` is the count of identical sequences sharing taxonomic labels—interpreting duplicates as empirical validation.
+- `SequenceTrustSlice`: Computes *global* confidence via pairwise alignment distances (LCSS scores) among group members.  
+  - Normalizes observed intra-group distance by the median pairwise distance across all groups (`obicleandb_median`).  
+  - Estimates effective sample size (`obicleandb_trusted_on`) using group composition and redundancy.
+
+### 4. **Higher-Rank Discrimination (Mann–Whitney U Test)**
+- `MakeSequenceFamilyGenusWorker` tests whether a sequence’s alignment scores to conspecifics are significantly better than to outgroups at genus/family level.
+- Uses `obialign.FastLCSScore` for rapid approximate alignment scoring on grouped sequences.
+- Outputs a *p*-value stored in `obicleandb_trusted`, indicating confidence that the sequence belongs to its assigned higher-rank taxon.
+
+### 5. **Efficient Distance Storage**
+- `diagCoord` implements compact triangular indexing for pairwise distance matrices, reducing memory footprint by ~50% while enabling fast lookup.
+
+### 6. **Pipeline Orchestration**
+- `ICleanDB` unifies all steps: input → taxonomy loading → filtering/dereplication → trust scoring.
+- Returns an iterator of cleaned, annotated sequences with standardized attributes.
+
+## Output Attributes
+
+| Attribute | Description |
+|----------|-------------|
+| `obicleandb_trusted` | Final confidence score (probability of correct taxonomic assignment) |
+| `obicleandb_trusted_on` | Effective group size used for scoring (accounts for redundancy) |
+| `obicleandb_level` | Taxonomic rank used in discrimination test (`genus`, `family`, or `"none"`) |
+| `obicleandb_median` | Median pairwise LCSS distance used as normalization baseline |
+
+## Design Principles
+
+- **Modularity**: Workers (e.g., `SequenceTrust`, `MakeSequenceFamilyGenusWorker`) are composable and reusable.
+- **Parallelism**: Batched processing via `obidefault` settings for scalability across large datasets.
+- **Robustness**: Gracefully handles sparse taxonomy, small group sizes, and missing labels.
+
+This package enables rigorous pre-processing of metabarcoding datasets—critical for reducing false positives in OTU/ASV inference and ecological interpretation.