I fixed one bug which was that the method getBinSize was failing when there was only one bin.
I do not manage to fix the other bug with the nan_bins:
I put an example with one interaction (one_interaction_4chr.cool):
chr1 10000 chr1 200000
with bins of 50k.
So one interaction between bin 0 and bin 3
with cool.load()
I get a matrix with a 1 in matrix[0][3], so in indices I have 3 and in nan_bins I have 0, 1, 2, 4, ...
In HiCMatrix, there is first cool.load, then fillLowerTriangle().
After this operation, indices become 0 and 3 perfect but the nan_bins are not adjusted.
For the moment, it looks like cool is the only format to support use nan.
Should I modify fillLowerTriangle?
Hi,
getBinSizewas failing when there was only one bin.chr1 10000 chr1 200000with bins of 50k. So one interaction between bin 0 and bin 3 with cool.load() I get a matrix with a 1 in matrix[0][3], so in indices I have 3 and in nan_bins I have 0, 1, 2, 4, ... In HiCMatrix, there is first cool.load, then fillLowerTriangle(). After this operation, indices become 0 and 3 perfect but the nan_bins are not adjusted. For the moment, it looks like cool is the only format to support use nan. Should I modifyfillLowerTriangle?