Add support for CRAMs

[mbookman]

IGV.js does not support CRAMs directly, but does support htsget.
It would be great if the htsget server could support CRAMs.
I know this is listed in the README:

CRAM support will be added in the very near future.

but wanted to make the explicit request.

[dglazer]

Do we know if htsget support for CRAM will automatically make it work for IGV? IIUC, htsget doesn't do any format conversion, so IGV would still need to have CRAM-aware code, even if it doesn't need to read the files directly.

[mbookman]

No, you are correct. IGV.js would still need to be CRAM aware.

Will follow-up with Jim to see if he has plans to make revisit igvteam/igv.js#247 or if having server-side conversion such as https://github.com/igvteam/igv.js-flask will be the solution for the foreseeable future.

Thanks for pointing this out.

[kemp-google]

Just to add we have a pull request that adds it we just haven't merged it yet

#19

[mbookman]

Thanks. BTW, on igvteam/igv.js#247, Jim has indicated that having server-side is the plan until someone writes a CRAM decoder for JavaScript.

[kemp-google]

A note to myself to update

https://github.com/samtools/hts-specs/blob/master/htsget_interop.html

when we merge this

[brainstorm]

AFAIK IGV.js does support CRAM at the moment of writing this:

https://igv.org/web/release/2.3.3/examples/cram.html