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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)
27 lines
2.0 KiB
Markdown
27 lines
2.0 KiB
Markdown
# Semantic Description of `obichunk` Package
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The `obichunk` package provides a flexible and configurable options management system for data processing pipelines, particularly in the context of biological sequence analysis (e.g., metabarcoding). It defines a typed `Options` struct and associated builder-style configuration functions.
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## Core Concepts
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- **Immutable Configuration Builder**: Options are constructed via `MakeOptions([]WithOption)`, applying a list of functional setters (`WithOption`) to an internal `__options__` struct.
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- **Encapsulation**: The concrete options are hidden behind a pointer (`pointer *__options__`) to ensure safe sharing and mutation control.
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## Supported Functionalities
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- **Categorization**: `OptionSubCategory(keys...)` appends category labels (e.g., sample or marker names) to an internal list; `PopCategories()` retrieves and removes the first category.
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- **Missing Value Handling**: `OptionNAValue(na string)` customizes placeholder for missing data (default: `"NA"`).
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- **Statistical Tracking**: `OptionStatOn(keys...)` registers statistical descriptions (via `obiseq.StatsOnDescription`) for per-field metrics collection.
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- **Batch Processing Control**:
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- `OptionBatchCount(number)` sets the number of batches.
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- `OptionsBatchSize(size)` defines how many items per batch (default from `obidefault`).
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- **Parallelization**: `OptionsParallelWorkers(nworkers)` configures concurrency level (default from environment).
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- **Disk vs Memory Sorting**: `OptionSortOnDisk()` enables disk-backed sorting; `OptionSortOnMemory()` disables it (default).
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- **Singleton Filtering**: `OptionsNoSingleton()` excludes singleton sequences; `OptionsWithSingleton()` allows them (default).
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## Design Highlights
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- Functional options pattern for extensibility and readability.
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- Default values derived from `obidefault` where applicable (e.g., batch size, workers).
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- Designed for integration with `obiseq` and `obidefault`, supporting scalable, reproducible NGS data workflows.
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