[hts-users:03757] small bug in HHEd

[Matt Shannon <sms46@xxxxxxxxx>]

Hi,

There is a small bug in clustering which results in slightly incorrect 
behaviour when variance flooring is used.

In the AccSumProb function in HHEd.c the line:

>     x+=-0.5*occ*(1.0+log(TPI*variance));

computes the auxiliary function value given a re-estimated parameter 
variance.  However this expression is only correct in the case of no 
variance flooring.

I have confirmed that this leads to a different number of leaves being 
chosen in some cases (for the autoregressive HMM, but the same should be 
true for the standard HMM).

Thanks,

Matt