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This commit adds an explicit --interleaved flag so paired reads can be consumed from a single file path or from stdin as one ordered stream. To preserve backwards compat, it keeps the existing paired-file behavior unchanged and preserves the current "- -" stdin form as an alternative way to request interleaved processing. Interleaved inputs can be written either as interleaved output or split across --output and --output2, matching the existing paired-output behavior. To coach the user toward correct usage, we use clap to reject invalid CLI combinations by erroring when --interleaved is used together with a second input file, and avoid warning on --output2 when interleaved mode is explicitly requested. And finally, the commit also adds tests covering interleaved paired input from a file, split output for interleaved input, and invalid use of --interleaved with a second input file.
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Summary
--interleavedflag so paired reads can be consumed from a single file path or stdin as one ordered stream"- -"stdin form as a non-breaking way to request interleaved processingTesting