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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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[BUG REPORT] hicCorrelate #765

Open jianglinghan opened 2 years ago

jianglinghan commented 2 years ago

When I run hicCorrelate, it repeatitively return the message below:

image

I checked my input, which seems fine with no Nan included. When browsing "hicCorrelate.py", I found that the diagnal of matrix set to 0 in line 282.

image

BUT when I observed it in ipython and found that the matrix was set to NULL after this step, since then, the object "_mat" is always NULL.

image

After 282 was commented, it seems work fine? Is it a bug or I misunderstood something? Please check it and feed me back. Many thanks :-)

My version: image

My command: image

joachimwolff commented 2 years ago

Hi jianglinghan,

I needed to dig here a bit in source code. We set the main diagonal to 0, but not the whole matrix. Can it be a coincidence that your matrix has only values at the main diagonal? In this case you would get the observed behaviour.

Best,

Joachim