I know there has been some discussion recently of HTSJDK releases, and upgrading to 4.3.0 (which was released, but not clearly tagged and release-noted).
I wanted to bring your attention to the fact that I just released HTSJDK 5.0.0. There are comprehensive release notes. You may want to look at it as it provides significant performance improvements in CRAM reading speed (and also BAM reading speed on non-x86 platforms), while also fixing a number of samtools/htslib interoperability issues.
I know there has been some discussion recently of HTSJDK releases, and upgrading to 4.3.0 (which was released, but not clearly tagged and release-noted).
I wanted to bring your attention to the fact that I just released HTSJDK 5.0.0. There are comprehensive release notes. You may want to look at it as it provides significant performance improvements in CRAM reading speed (and also BAM reading speed on non-x86 platforms), while also fixing a number of samtools/htslib interoperability issues.