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https://github.com/metabarcoding/obitools4.git
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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)
48 lines
2.0 KiB
Markdown
48 lines
2.0 KiB
Markdown
# OBIOptions Package: Global Command-Line Interface Utilities
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The `obioptions` package provides shared command-line argument parsing and runtime configuration for OBITools4 commands. It centralizes common options, logging setup, profiling controls, and taxonomy handling.
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## Core Functionalities
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- **Global Option Registration**: `RegisterGlobalOptions()` defines shared flags such as:
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- `--version`, `--debug`
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- CPU/thread control (`--max-cpu`)
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- Batch processing parameters: `--batch-size`, `-size-max`, `--batch-mem`
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- Quality encoding (`--solexa`)
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- Warning suppression (`--silent-warning`)
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- **Option Processing**: `ProcessParsedOptions()` handles post-parsing logic:
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- Prints help/version and exits on request
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- Loads default taxonomy via `obiformats.LoadTaxonomy()`
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- Configures log level (debug/info)
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- Starts `pprof` HTTP servers for performance profiling:
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- Generic (`/debug/pprof`)
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- Mutex contention (`--pprof-mutex`, `runtime.SetMutexProfileFraction()`)
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- Goroutine blocking (`--pprof-goroutine`, `runtime.SetBlockProfileRate()`)
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- **Parser Generator**: `GenerateOptionParser()` builds a reusable argument parser with:
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- Bundled short options (`-abc`)
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- Strict unknown-option handling
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- Automatic `--help` support
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## Taxonomy Integration
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- `LoadTaxonomyOptionSet()` registers taxonomy-specific flags:
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- Required/optional path to DB (`--taxonomy`, `-t`)
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- Alternative names search (`--alternative-names`)
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- Taxonomic validation: `--fail-on-taxonomy`, automatic updates via `--update-taxid`
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- Raw taxID output (`--raw-taxid`)
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- Leaf sequences inclusion via `--with-leaves`
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## Runtime Accessors
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- `CLIIsDebugMode()`, `SeqAsTaxa()` → read current state
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- `SetDebugOn/Off()` → programmatic debug toggling
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## Design Principles
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- Environment variable support (`OBIMAXCPU`, `OBIWARNING`, etc.)
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- Thread-safe taxonomy loading with mutex
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- Graceful error handling (parse errors → help + exit)
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- Integration with `logrus` and Go’s standard profiling tools
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