Add support for CRAMs
mbookman opened this issue · 6 comments
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.
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.
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.
Just to add we have a pull request that adds it we just haven't merged it yet
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.
A note to myself to update
https://github.com/samtools/hts-specs/blob/master/htsget_interop.html
when we merge this
AFAIK IGV.js does support CRAM at the moment of writing this: