`--skipNonCoveredRegions`/`--skipNAs` not working for `bigwigCompare` in sparse data

[jantusan]

Hello,

I have DNA methylation bigwigs with single cytosine resolution and I am trying to reduce the size of the files by averaging the methylation values across bins. I found that bigwigCompare can take the same bigwig twice and average the signal across bins using this command:

$ bigwigCompare --operation mean -b1 wt_CG.bw -b2 wt_CG.bw -o wt_CG_bins.bw

However, methylation data is discontinuous and there may be regions with no cytosines that shouldn't be considered as having zero signal (the default behaviour of Deeptools), so I added the flag --skipNonCoveredRegions. But this gives me the following error:

$ bigwigCompare --operation mean --skipNonCoveredRegions -b1 wt_CG.bw -b2 wt_CG.bw -o wt_CG_bins.bw
[bwClose] There was an error while finishing writing a bigWig file! The output is likely truncated.

I tried using different methylation input file, and two different bigwigs for -b1 and -b2 but I got the same error.

I am not sure if this is limited to sparse data like DNA methylation, but it would be great if the --skipNonCoveredRegions worked as otherwise the methylation level is underestimated on wider regions as a lot of bins with no data in it are now zero.

$ deeptools --version
deeptools 3.1.3
$ python --version
Python 3.8.2