3DGenomes/tadbit — pull request #23 by gui11aume (2013-10-08 18:37:41+00:00)
Title: Tentative fix of an underflow bug with visibility normalization.

The visibility normalization caused an erratic bug which gave extremely small TADs all over chromosome in an unpredictable way. I could trace it down to an underflow problem caused by taking the log of visibility weights, which are sometimes too close to 0. In the end, all the computed likelihood were 'nan' in which case the selection of the best state was always the maximum number of TADs.

The current fix is to scale up the weights in the range where they will hopefully not cause underflow. If there is no underflow, scaling the weights to any value does not change the outcome of TADBit.

First, the current fix has to be tested on real HiC data, second, a routine check for underflow should be done and weights should be re-scaled in case that happens.