Re: [Seqan-dev] Disk-based index

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

Hi Jochen,

Thanks for the quick response.

On 13/09/13 11:44, Singer, Jochen wrote:

Hi John,

we use the indices in some application targeted at mapping reads to human reference genomes. Therefore all indices should work on large data sets. Could you provide some more information on the problem you are running into?

I'll try and dig a bit deeper into it.

Concerning the large number of files which are created I assume you are using an index build over a StringSet. The save function stores each String in the StringSet into a separate file. However, if you specify the StringSet to be a ConcatDirect StringSet, (StringSet<TString, Owner<ConcatDirect<> > >

) then all strings are concatenated internally and only tow file is stored (one with the sequence and one with the sequence length information).

Thanks for the tip regarding the stringset. I'm not sure I can change my code so easily to use that but I'll have a look.

At the moment there is no compression of the index files available, you would have to do it manually, but its a thought we should keep in mind.

I might well do it myself then.

I hope that helps!

Thanks!
John.