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