On Sat, 2011-06-25 at 07:05 -0400, David Eccles (gringer) wrote: > Sebhtml wrote: > > KmerAcademy is a place where all k-mer must transit before making it > > to the GridTable. Those observed only once remain in the > > KmerAcademy. This academy is then destroyed. > > YES! Thank you for implementing this, I expect that this should make a > substantial impact on memory usage, and the quality of the output assembly.
Yes it does ! ;) > Just to explain my expectations, one of my friends worked at the > National archives in New Zealand and did a study on access counts for > things that were stored in the library. He found that items that hadn't > been accessed in the last five years were extremely unlikely to ever be > accessed again -- basically, things that are only rarely accessed are a > really good candidate for being stored in the bottom of a locked filing > cabinet stuck in a disused lavatory with a sign on the door saying > 'Beware of the leopard'. > There is a data structure for that: the splay tree. http://en.wikipedia.org/wiki/Splay_tree > I've since had a suspicion that this phenomena applies to many different > areas, particularly those involving databases, and statistics on the > Kmer academy should help me to work out if this is also true for genome > assembly. > Yes. I think (I might be wrong) that Velvet was the first software in genomics to use splay trees. In Ray, I implemented a grid table with a similar behaviour but without the allocation overhead of pointers. > Regards, > -- David Eccles > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense.. > http://p.sf.net/sfu/splunk-d2d-c1 > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
