Fastq chunks fix

[wwood]

No description provided.

[chatgpt-codex-connector]

💡 Codex Review

singlem/singlem/utils.py

Line 117 in bf15f19

raise Exception(f"Cannot determine format (FASTA or FASTQ) for chunking from file extension: {path}")

Preserve chunking for extensionless streamed inputs

The new format check in prepare_chunking_fifos now hard-fails when the path does not end in .fa/.fasta/.fna/.fq/.fastq after suffix stripping, which regresses chunking for valid streamed inputs such as FIFOs or process-substitution paths (for example /dev/fd/*) that often have no extension. Before this commit those inputs were still chunked (as FASTA semantics), but now --read-chunk-size/--read-chunk-number aborts immediately even when the underlying data is valid, breaking chunked workflows that rely on extensionless paths.

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