Chris Norman

Closed via https://github.com/broadinstitute/gatk/pull/8035.

Also, the 4.x versions of the vcf spec all state that GQ is an integer. Having said that, according to github, the particular line referenced above is *8* years old,...

Right, thanks for the link. Perhaps there is some compelling reason to do otherwise, but my suggestion would be to have the default behavior be to preserve the scheme that...

@ohofmann Hi Oliver - yes, this PR addresses quite a few issues with VCF support in htsjdk, and is a prerequisite for a couple of other large PRs for VCF/BCF...

@lbergelson I've rebased this on master/Java 17.

@lindenb This PR is dependent on both https://github.com/samtools/htsjdk/pull/1581 and https://github.com/samtools/htsjdk/pull/1596. I wish I could be more definitive - I still hope to get these merged somehow, but until then this...

We're integrating this as part of Yash's codecs PRs.

@bw2 For better or worse, htsjdk tries to maintain round-trip fidelity for CRAMs. I took a look at the first few slices of the CRAM referenced above, and it does...

The underlying issue here is is that the GATK conda env environment isn't established since bioconda doesn't appear to configure it. The NPE needs is fixed by #7816. In this...

@felixm3 The bioconda environment doesn't actually configure the gatk conda environment (it installs gatk, but not the python dependencies required for CNNScoreVariants). You need to set up the gatk conda...