Re: [Seqan-dev] Random access of large FASTA file

["Weese, David" <weese@campus.fu-berlin.de>]

Am 21.07.2011 um 17:26 schrieb Johannes Dröge:

> Thanks for you nice explanation. So open() is the magic function do apply to a ConcatDirect StringSet. Sorry for bugging you further, before I start with the implementation I have some final questions...
> 

Actually, you don't call open with the StringSet but both of its members limits and concat.

> My primary target is the in-memory sequence storage, as I wrote, so for this I do not need to specialize the limits object. I suppose open() works with regular Alloc strings as well?
> 

Yes, but before need to call save() before destructing the String to synchronize changes in the string with the file on disk.

> Where are temporary MMap files usually stored?

In the system-wide temporary folder, unless you defined a different folder in the environment variable TMPDIR.

> 
> Can I somehow use read-only file access with persistent MMap files?

Yes, see:
http://www.seqan.de/dddoc/html_devel/FUNCTION.open.html

> 
> Gruß Johannes
> 

Gruß,
David