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Reviewed commit: f578e271d6
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| if base.endswith('.gz'): | ||
| base = base[:-3] | ||
| if base.endswith(('.fq', '.fastq')): |
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prepare_chunking_fifos now strips only .gz before checking FASTA/FASTQ suffixes, so non-.gz compressed names fall through to the new exception path. In SearchPipe.run, chunking is applied after prepare_zstd_fifos, which renames zstd inputs to FIFOs like *.zst.fifo; with --read-chunk-size/--read-chunk-number, these files no longer match the FASTA/FASTQ suffix checks and the pipeline aborts instead of chunking reads. This introduces a regression for chunked zstd input workflows.
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