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Published 20 hours ago • verified publisher icon googlegenomics

Add support for CRAMs

Open mbookman opened this issue 7 years ago • 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.

mbookman avatar Feb 23 '18 18:02 mbookman

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.

dglazer avatar Mar 06 '18 01:03 dglazer

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 https://github.com/igvteam/igv.js/issues/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.

mbookman avatar Mar 06 '18 16:03 mbookman

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

https://github.com/googlegenomics/htsget/pull/19

kemp-google avatar Mar 06 '18 19:03 kemp-google

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

mbookman avatar Mar 06 '18 19:03 mbookman

A note to myself to update

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

when we merge this

kemp-google avatar Mar 12 '18 19:03 kemp-google

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

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

brainstorm avatar Oct 31 '19 00:10 brainstorm