Re: [Seqan-dev] Disk-based index

[John Reid <j.reid@mail.cryst.bbk.ac.uk>]

Hi Enrico,

On 28/08/13 10:46, Siragusa, Enrico wrote:

Hi John,

On Aug 28, 2013, at 10:54 AM, John Reid <j.reid@mail.cryst.bbk.ac.uk>

 wrote:

Hi all,

I would like to index the mouse or human genome with an ESA. I need to do this more than once though and would like to store the ESA on disk as it takes some hours to construct. Is this feasible? Is there any way to do this in SeqAn already?

Sure. To save an index after constructing it, you can call save(index, "/path/to/index"). To load it, call open(index, "/path/to/index"). The path must be given as a C style string, so if you're using a SeqAn String, please use toCString() to convert it.

Do you have any experience using this functionality with genome sized indexes (3Gb or so)? Would you expect it to work? I seem to be running into some issues I need to debug. I was just wondering if anyone else had used it in this way. Also the save function seems to create many files in the same directory. I imagine this could be a problem for some filesystems. Might you consider changing this? Also as mentioned before the ability to save in a compressed format would be very attractive to me as well.

Thanks for all the great work in SeqAn,
John.