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⬆️ version bump to v4.5

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- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)
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Eric Coissac
2026-04-07 08:36:50 +02:00
parent 670edc1958
commit 8c7017a99d
392 changed files with 18875 additions and 141 deletions
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autodoc/docmd/pkg/obiformats/fastqseq_write_generic.md
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## Semantic Description of `obiformats` Package
The `obiformats` package provides core formatting utilities for biological sequence data in standard FASTX formats (FASTA and FASTQ). It defines two functional types:
- `BioSequenceFormater`: Converts a single biological sequence (`*obiseq.BioSequence`) into its string representation.
- `BioSequenceBatchFormater`: Converts a batch of sequences (`obiiter.BioSequenceBatch`) into raw bytes, suitable for file or stream output.
Two main constructor functions enable flexible formatting:
- `BuildFastxSeqFormater(format, header)` returns a sequence-level formatter based on the requested format (`"fasta"` or `"fastq"`), applying optional header metadata via `FormatHeader`.
- `BuildFastxFormater(format, header)` builds a batch formatter by composing the sequence-level function over all sequences in an iterator-driven batch, concatenating results with newline separators.
The package supports extensibility and type safety through function composition while integrating logging (via `logrus`) for critical errors—e.g., unsupported formats trigger a fatal log. It abstracts away low-level I/O, focusing purely on *semantic formatting logic*, making it ideal for pipeline integration in NGS data processing tools.