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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)
40 lines
2.1 KiB
Markdown
40 lines
2.1 KiB
Markdown
# Semantic Description of `obiseq` Statistics and Merging Features
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This package provides infrastructure for **tracking, aggregating, and merging statistical occurrences** of sequence attributes across biological sequences (`BioSequence`). It supports both **count-based and weighted statistics**, with thread-safe operations.
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## Core Components
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- `StatsOnValues`: A concurrent map (`map[string]int`) with R/W locking to store occurrence counts per attribute value (e.g., taxon, primer, quality bin).
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- `StatsOnDescription`: Defines *how* to extract and weight statistics from a sequence (e.g., count per read, or sum of quality scores).
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- `StatsOnSlotName(key)`: Generates internal annotation keys (e.g., `"merged_taxon"`) to store precomputed statistics.
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## Key Functionalities
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1. **Per-Sequence Statistics Initialization & Update**
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- `StatsOn(desc, na)`: Ensures a statistics slot exists for attribute `desc.Key`, initializes if needed.
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- `StatsPlusOne(...)`: Adds contribution of a *single* sequence to the statistics (e.g., increment count for its taxon).
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2. **Thread-Safe Aggregation**
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- `Merge(*StatsOnValues)`: Safely merges counts from another `StatsOnValues`, used to combine per-sequence stats.
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3. **Sequence Merging with Stat Propagation**
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- `BioSequence.Merge(...)`:
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- Combines two sequences (e.g., consensus/overlap).
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- Updates statistics for specified attributes (`statsOn`), preserving or aggregating counts.
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- Resolves conflicting annotations by deleting non-merged fields if mismatched.
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4. **Bulk Merging**
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- `BioSequenceSlice.Merge(...)`: Efficiently merges *N* sequences into one, recycling inputs and updating statistics incrementally.
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## Use Cases
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- Tracking taxonomic assignments across merged reads.
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- Aggregating primer or barcode counts in amplicon merging.
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- Summarizing quality scores, abundance weights, or custom metadata during consensus building.
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## Design Notes
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- Uses `sync.RWMutex` for safe concurrent access.
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- Supports only JSON-marshalable, serializable statistics (via `MarshalJSON`).
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- Enforces type safety: only strings/integers/booleans allowed for attribute values.
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