mirror of https://github.com/metabarcoding/obitools4.git synced 2026-04-30 12:00:39 +00:00

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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

Semantic Description of `obiformats` Package

The obiformats package provides utilities for parsing sequence headers in the OBItools4 framework, supporting two distinct formats:

JSON-based format (e.g., {"id":"seq1", ...}): Detected by a leading { character.
Legacy OBI format (plain text, e.g., >seq1 description): Used when no JSON prefix is present.

Core Functions

ParseGuessedFastSeqHeader(sequence *obiseq.BioSequence)
Dynamically routes header parsing based on the first character of the sequence definition:
- Calls ParseFastSeqJsonHeader if JSON-prefixed.
- Otherwise invokes ParseFastSeqOBIHeader.
IParseFastSeqHeaderBatch(iterator, options...) obiiter.IBioSequence
Applies header parsing to a batch of sequences:
- Takes an iterator over BioSequences.
- Uses optional configuration (e.g., parallelism, parsing behavior).
- Wraps the parser in a worker pipeline via MakeIWorker, preserving sequence flow.

Format agnosticism: Automatically detects header type.
Iterator-based streaming: Enables memory-efficient batch processing of large datasets (e.g., FASTQ/FASTA).
Extensibility: Options pattern (WithOption) supports runtime customization.

This package serves as a header-decoding layer for downstream analysis in metagenomic or metabarcoding workflows.