Nezar Abdennur

It sure does! [`cooler dump`](https://cooler.readthedocs.io/en/latest/cli.html#cooler-dump) is what you are looking for. See the `--range` option.

For example, to invert the `KR` one, open the underlying HDF5 file in append mode and save a new column: ```python clr = cooler.Cooler(...) with clr.open('r+') as f: f["bins"].create_dataset("KR_mult", data=1./f["bins/KR"][:],...

Yes, it's probably a mismatch between the names used in the cooler file and/or the names used in `gc_cov` and `view_df`, rather than the .fa itself. You can rename chrom...

I suspect it is a file system issue. I'm assuming `/store/` is some kind of mounted network drive or has limited permissions, and cooler is attempting to use it for...

> I don't think it has changed where tmp file were created BTW All the more reason to expose it via a command line option. I haven't tested it myself...

Yeah, my bad. The file is first written in "a" or "w" mode and closed, then re-opened in "r+" mode where the error occurs at line 616: https://github.com/open2c/cooler/blob/master/cooler/create/_create.py#L572-L616 So the...

Hi @nservant, > I have a bed file with genomic intervals of 1kb, from chrX:150125000-153125000 Bin tables must start at 0 and should end at the chromosome length, even if...

Looks like the joblib folks have extracted it out into a separate tool now: https://github.com/joblib/threadpoolctl And numpy is working on providing something internally: https://github.com/numpy/numpy/pull/13136

Cooler URI refers to the filepath + optional resource path within the file, described [here](http://cooler.readthedocs.io/en/latest/api.html#uri-string). Direct HTTP access is not supported yet.

I'm okay with this. It provides an explicit default. The alternative would be to have a hybrid store argument that takes a bool or a string. `store=True` would use an...