Implement support for creating CRAI files

[cmnbroad]

Ideally, both from an existing CRAM file and on-the-fly during CRAM writing. @vadimzalunin it looks like this is implemented in cramtools - do you know if any reason that implementation couldn't be moved to htsjdk ? I've looked at it a bit and am happy to do the work.

[vadimzalunin]

I think it was agreed before that we focus on BAI rather than CRAI in htsjdk to avoid confusion. But I'm :+1 on full CRAI support.

[GWarsow]

Ideally, both from an existing CRAM file and on-the-fly during CRAM writing. @vadimzalunin it looks like this is implemented in cramtools

Creation of cram index files during CRAM writing is not yet supported in cramtools (neither bai nor crai). I commented on this just to avoid that others may get confused when they read above cited statement.

Best
Gregor

[cmnbroad]

Update: there is now support for creating .crai (#538), but its not currently turned on by default due to #531.