HTSJDK 4.3.0 for CRAM v3.1 support

[dkj]

The intention is to help EBI accept CRAM v3.1. The required functionality is available in the 4.3.0 tag of htsjdk. I fear a 4.3.0 "release" is unlikely on any known timescale - there needs to be funding to support a development team.

[davidyuyuan]

Thank you for creating 4.3.0 tag with samtools/htsjdk#1739 included. As you know, ENA is a global production archive. The risk to use a PR outside a release is too high. We have to wait for the PR picked up in a release. There is no way around that. Thank you for your understanding.

[dkj]

Thank you for creating 4.3.0 tag with samtools/htsjdk#1739 included. As you know, ENA is a global production archive. The risk to use a PR outside a release is too high. We have to wait for the PR picked up in a release. There is no way around that. Thank you for your understanding.

Thanks for considering this @davidyuyuan and stating your position.

I recommend you should try to check-in with upstream - and depending on what you find out maybe make plans (to deal with contemporary and new versions of file formats) should the next likely htsjdk official release be many years away, or never happen at all. N.b. It's my (hopefully mis-) understanding of that [sad] situation which drove this PR.

[edit: As a global production archive, I would really like EBI/ENA to be able to deal with the almost 3 year old GA4GH CRAM v3.1 spec files.]