Speedy simulations

Our programming assistant has finished his work for us.  At least, he's finished the period when he's employed by us, but now he's gotten the research bug and wants to stay involved to see how the program he's developed for us works out.

At present it works great - MUCH faster than before.  One of the reasons is that it no longer scores the genome in every cycle.  I'm doing a run now with a big genome (100 kb) and I can see it pause at every 100th cycle, as it takes the time to score the genome.  This is a sensible improvement, as the genome score isn't needed for the progress of the simulation - it just lets us the user monitor what's happening, and provides information used if the run needs to decide whether it has reached equilibrium.

I'm using this run to test whether the final accumulated USS motif precisely matches the biases specified in the recombination decisions (i.e. in the matrix used to score each fragment), by using a matrix where one position has substantially weaker bias than the others.  If the final motif matches the matrix bias, this position should show a weaker consensus in the accumulated uptake sequences.  

Of course to test this I may have to recall how to run the Gibbs Motif Sampler on the Westgrid server.  The alternative is to chop my 100 kb output genome into 10 pieces and run each separately on the Gibbs web server, which has a sequence limit of 10 kb.