Chris Norman

Rebased on current master, and added a second commit to reflect the new test results that are presumably related to https://github.com/broadinstitute/gatk/pull/7394. I assume that the original issue (overwriting the expected...

Closing in favor of https://github.com/broadinstitute/gatk/pull/7963.

@davidbenjamin Sorry I've been out and just got around to looking at this. Given that this test appears to run just fine in the Java 11 job (which is not...

@doazen I need to re-review this myself, and see what more validation I can do. I hate to miss the release, but I won't be able to do that today.

@droazen I thought I had updated this months ago saying that I was finished validating, and that it was ready for review, but it appears that I didn't. But anyway...

Good idea. Another use case for this would be to take a bam/cram and set of references, and see if there is a reference suitable for the bam/cram, which would...

I'm not aware of any activity on this, unless @magicDGS is still pursuing it.

Closing in favor of a (coming soon) replacement.

Note: this needs to be resolved/updated to account for the final disposition of structured vs. unstructured lines, attribute ordering, and quoting, as described in https://github.com/samtools/hts-specs/issues/642/ https://github.com/samtools/htsjdk/issues/1610, and also https://github.com/samtools/hts-specs/pull/620.

I don't have any issue with changing `WeakReference` to `SoftReference`, if it somehow actually fixes a problem. Is there any evidence that it does ? The gatk code isn't (and...