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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)
65 lines
3.1 KiB
Markdown
65 lines
3.1 KiB
Markdown
# `obisummary` Package: Semantic Description
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The `obisumsummary` package delivers lightweight, high-performance statistical summarization of biological sequence data processed by OBITools4. It enables rapid profiling of metadata and content-level features across large sequence sets—especially useful post-processing (e.g., after `obiclean` or merging)—while supporting parallel execution for scalability.
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## Core Data Model
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- **`DataSummary` struct**: Central container tracking:
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- Global metrics: number of reads, unique variants (distinct sequences), and total symbols.
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- Presence flags for special annotations: `merged_sample`, `obiclean_status`/`weight`.
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- Categorized annotation metadata:
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- Scalar attributes (single-value per sequence).
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- Map-like tags (`map_tags`), where each key maps to counts.
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- Vector or vector-like attributes (multi-value per sequence).
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- Per-sample statistics: variant count, singleton detection, and `obiclean`-related flags (e.g., bad reads).
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## Low-Level Helpers
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- **Map aggregation utilities**:
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- `sumUpdateIntMap`: Accumulates integer values across maps.
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- `countUpdateIntMap`, `plusOne/PlusUpdateIntMap`: Increment counters for keys (e.g., attribute or sample names).
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- **`Add()` method**: Thread-safe merge of two `DataSummary`s—enables parallel accumulation.
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## Main Processing Logic
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- **`Update()` method**: Processes one `BioSequence`, updating:
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- Read count (via `.Count()`) and sequence-level metrics.
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- Variant detection via unique sequences; symbol count (total length).
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- Sample-aware logic: detects `merged_sample` or per-sample annotations to populate sample-level stats (e.g., singleton identification).
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- Annotation classification: routes keys into scalar, map, or vector buckets.
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- **`ISummary()` function**: Parallel summarization engine:
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- Distributes work across `nproc` goroutines.
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- Aggregates partial summaries via atomic operations (`Add()`).
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- Returns a structured map with:
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```json
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{
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"count": { "variants", "reads", "total_length" },
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"annotations": {
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"scalar_attributes",
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"map_attributes",
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"vector_attributes",
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"keys": { scalar: {...}, map: {...}, vector: {...} }
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},
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"samples": {
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"sample_count",
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"sample_stats": { sample_name: { reads, variants, singletons [, obiclean_bad] } }
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}
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}
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```
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## CLI Integration (`obisummary` subpackage)
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- **Option registration**:
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- `SummaryOptionSet()`: Registers flags for output format (`--json-output`, `--yaml-output`) and map attributes to summarize (`-map <attr>`).
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- `OptionSet()`: Extends above with input-handling options (e.g., file/iterator sources) from `obiconvert`.
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- **Runtime introspection**:
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- `CLIOutFormat()`: Returns `"yaml"` (default) or `"json"`, with YAML only active if JSON is *not* requested.
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- `CLIHasMapSummary()` / `CLIMapSummary()`: Check and retrieve requested map attributes.
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- **Design notes**:
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- Uses global state (e.g., `__json_output__`, `__map_summary__`) for compatibility with [`go-getoptions`](https://github.com/DavidGamba/go-getoptions).
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- Scope strictly limited to CLI configuration—no data processing logic resides here.
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