>I think we need to develop a utility that will take these files, split them by chromosome, sort, index them for random access, and then save them,  with the default index, to disk. 

I think this is precisely what the DAS/2 indexing scheme I wrote does.

I'm not aware of any problems with the DAS/2 server; iIt should be just fine with large files.  Please send me more details.

Thanks,
John

On Fri, Oct 23, 2009 at 11:42 AM, David Nix <david.nix@hci.utah.edu> wrote:
Hey Folks,

I’ve been loading a lot of huge bed files into the DAS/2 server and I think it is crushing the app.  I think we need to develop a utility that will take these files, split them by chromosome, sort, index them for random access, and then save them,  with the default index, to disk.  Lastly, build this new binary bed file format into IGB and the DAS/2 server. I might be able to hack Gregg’s bar file indexing scheme to do this but was hoping someone with more programming skills could look into it.  Google protocol buffers? UCSC’s bigBed format (they’ve done a fair bit of work along these lines and might be willing to share their code)?

Volunteers?  

Help!

-cheers, David


--
David Austin Nix, PhD | HCI Bioinformatics | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | david.nix@hci.utah.edu | http://bioserver.hci.utah.edu

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