Add FastqFile.Offset enum

[ehsanestaji]

Summary

• Add a nested FastqFile.Offset IntEnum for the supported FASTQ quality-score encodings.
• Use the enum in the constructor, read(), read_iter(), and write_iter() type hints and documentation.
• Update biotite.application.sra to expose the same offset API.
• Continue accepting integer offsets while removing the legacy string aliases for Biotite v2.

Motivation

The enum makes the supported FASTQ variants discoverable while mapping directly to their numeric ASCII offsets. Since this change targets Biotite v2, the legacy string aliases are removed rather than carried forward as compatibility behavior.

Validation

• pixi run -e test test tests/sequence/test_fastq.py -q — 23 passed
• pixi run lint

Closes #923

[padix-key]

Thanks for tackling the issue! This change is planned for v2 of Biotite (I also changed the target branch of this PR), so we do not need to keep the string values for compatibility reasons. Note that biotite.application.sra needs to be updated as well as it exposes the same offset values.

[padix-key]

Without the need of the legacy names I think this test can be omitted.

[ehsanestaji]

Addressed in eb4753b7 — I removed the obsolete legacy-string test. The broader update also applies FastqFile.Offset throughout biotite.application.sra. Validation: 23 FASTQ tests passed and pixi run lint completed successfully.

[codspeed-hq]

Merging this PR will improve performance by 13.39%

⚡ 5 improved benchmarks
✅ 98 untouched benchmarks
⏩ 14 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
⚡	benchmark_match_kmer_selection[BucketKmerTable(10000)-None]	353.3 µs	304.1 µs	+16.18%
⚡	benchmark_match[BucketKmerTable(10000)-None]	401.2 µs	352.2 µs	+13.91%
⚡	benchmark_match_kmer_selection[KmerTable-None]	278.3 µs	245.7 µs	+13.29%
⚡	benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]	275.3 µs	244.5 µs	+12.58%
⚡	benchmark_match[KmerTable-None]	327 µs	294.5 µs	+11.03%

Tip

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_{Comparing ehsanestaji:feat/923-fastq-offset-enum (eb4753b) with main (1fa1b70)²}

Footnotes

1. 14 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

2. No successful run was found on v2 (1fa1b70) during the generation of this report, so main (1fa1b70) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩