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

Semantic Description of obiformats Package Functionalities

The go package obiformats provides a flexible, configuration-driven framework for handling biological sequence data (e.g., FASTA/FASTQ) and associated metadata. Its core component is the Options type, which encapsulates user-defined settings via an immutable configuration pattern using functional setters (WithOption).

Key capabilities include:

• I/O control: file handling options (e.g., OptionCloseFile, OptionsAppendFile), compression support (OptionsCompressed), and batch processing modes (e.g., FullFileBatch, custom BatchSize).
• Parallelism & performance tuning: configurable number of workers (OptionsParallelWorkers) and memory buffer size (via TotalSeqSize).
• Sequence parsing/formatting: pluggable header parsers/writers for FASTA/FASTQ (e.g., OptionsFastSeqHeaderParser, OptionFastSeqDoNotParseHeader), with support for quality scores (OptionsReadQualities).
• CSV export: granular control over columns (ID, sequence, quality, taxon, count), separators (CSVSeparator), NA values (CSVNAValue), and auto-inferred keys (CSVAutoColumn).
• Taxonomic metadata integration: toggles for taxid, scientific name, rank, path (with/without root), parent relationships (OptionsWithTaxid, OptionWithoutRootPath), and U→T conversion for ambiguous bases.
• Advanced features: feature table inclusion (WithFeatureTable), pattern matching support (OptionsWithPattern), and paired-end read handling via WritePairedReadsTo.
• Metadata extensibility: arbitrary metadata fields can be attached via OptionsWithMetadata, with automatic cleanup (e.g., removal of "query" when pattern mode is active).

All options are initialized with sensible defaults (e.g., batch_size, parallel_workers) and can be composed using the MakeOptions constructor. This design enables declarative, reusable configuration across sequence processing pipelines in OBITools4.