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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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VCF sorting change breaks existing VCFs #1637

Open lbergelson opened 1 year ago

lbergelson commented 1 year ago

I failed to consider the effect of changing the VCF sort order on processing existing VCFs when merging https://github.com/samtools/htsjdk/pull/1593. This breaks many things.

I think this is still a good idea but we need to reconsider how to do it safely, possibly a split comparator with different levels of sorting vs validating like the sam sort orders use.

The commit e2943b78ff595e144281b8a3c126be5a4d70085d reverts https://github.com/samtools/htsjdk/pull/1593.

This blocks https://github.com/samtools/htsjdk/pull/1629 as well.

lbergelson commented 1 year ago

@clintval Sorry, I rolled your change back for now. I'd like to get it back in but it might take me a bit to get to it.