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Change queryname sort to match samtools #1601

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@nh13 nh13 commented Mar 30, 2022

This PR is meant to start a discussion to standardize the queryname sort order between samtools and htsjdk. It is a constant source of confusion, and sometimes problems, especially when trying to use the output of multi-threaded samtools sort -n going into picard/gatk/htsjdk.

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I'm in favor of fixing this embarrassing and long standing problem. This would be a compatibility nightmare though as I'm sure you're aware... Should we consolidate this discussion in Tim's PR?

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