Change queryname sort to match samtools #1601
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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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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 -ngoing into picard/gatk/htsjdk.