obitools4/autodoc/docmd/pkg/obioptions/options.md

OBIOptions Package: Global Command-Line Interface Utilities

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.

Core Functionalities

• Global Option Registration: RegisterGlobalOptions() defines shared flags such as:

  • --version, --debug
  • CPU/thread control (--max-cpu)
  • Batch processing parameters: --batch-size, -size-max, --batch-mem
  • Quality encoding (--solexa)
  • Warning suppression (--silent-warning)

• Option Processing: ProcessParsedOptions() handles post-parsing logic:

  • Prints help/version and exits on request
  • Loads default taxonomy via obiformats.LoadTaxonomy()
  • Configures log level (debug/info)
  • Starts pprof HTTP servers for performance profiling:
    • Generic (/debug/pprof)
    • Mutex contention (--pprof-mutex, runtime.SetMutexProfileFraction())
    • Goroutine blocking (--pprof-goroutine, runtime.SetBlockProfileRate())

• Parser Generator: GenerateOptionParser() builds a reusable argument parser with:

  • Bundled short options (-abc)
  • Strict unknown-option handling
  • Automatic --help support

Taxonomy Integration

• LoadTaxonomyOptionSet() registers taxonomy-specific flags:
  • Required/optional path to DB (--taxonomy, -t)
  • Alternative names search (--alternative-names)
  • Taxonomic validation: --fail-on-taxonomy, automatic updates via --update-taxid
  • Raw taxID output (--raw-taxid)
  • Leaf sequences inclusion via --with-leaves

Runtime Accessors

• CLIIsDebugMode(), SeqAsTaxa() → read current state
• SetDebugOn/Off() → programmatic debug toggling

Design Principles

• Environment variable support (OBIMAXCPU, OBIWARNING, etc.)
• Thread-safe taxonomy loading with mutex
• Graceful error handling (parse errors → help + exit)
• Integration with logrus and Go’s standard profiling tools