Change queryname sort to match samtools

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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Change queryname sort to match samtools #1601

Open nh13 opened 2 years ago

nh13 commented 2 years ago

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.

lbergelson commented 2 years ago

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?