--setToZeroThreshold 1.0 for normalization method smallest

[MWSchmid]

Hi there

Thanks for the tools, work really well so far. Just one point that caused quite some confusion. The manual for the normalization step says:

--setToZeroThreshold

"It is recommended to set it for the normalize mode “smallest” to 1.0."

I did so and observed that the smallest sample was very different from the rest by having much more inter-chromosomal interactions. I guess that choosing exactly 1.0 deletes most inter-chromosomal interactions in all samples except for the smallest. Hence, I wouldn't recommend choosing 1.0 and I would also think about disabling this threshold in the "smallest" mode.

Best,

Marc