On Oct 28, 2015, at 9:39 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
Just for mirabait?
Yep, just for mirabait.
Interesting what a single post can do. In short, the next release of MIRA
will have a revamped mirabait, with a 2^31bp limit in sequence lengths, but
which also will be quite a deal faster.
30kb limit in sequences? Oooops, I was using old routines. Changing to new
ones drops the limit and gives instant 25% boost in baiting speed.
Hmmm, loading takes quite long? A few tweaks here and there doubles the
loading speed.
These two steps alone reduce runtime by 40%.
But then … why is the baiting step not multithreaded? Oh wait, a simple
version is trivial to implement.
Result: with 4 cores, the new version is now 3x faster than the old one. Yay.
