Dario Beraldi

Hi- It's hard to tell what is happening without seeing more of the data. Check that chromosome names are consistent across the input files. Also have a look at the...

Try using [mamba](https://mamba.readthedocs.io/en/latest/installation.html) instead of conda (I should update the README). After installing it, instead of ``` conda install -c bioconda -c conda-forge cnv_facets ```` use ``` mamba install -c...

Can you give some details about your system? I googled *libgfortran.so.4: cannot open shared object file* and there may be some relevant hits you could try to follow.

Hello- apologies for keeping quiet... At the moment, I cannot reproduce the issue either locally or on github actions. I run the test suite on Ubuntu 20 and 22 and...

Hi Yingzi- Thanks for your interest in ASCIIgenome. > Now, I only need reads having indels on chr11:2699098-2699099. And I don't want to have reads only having SNVs on chr11:2699098-2699099....

@johanneskoester thanks for replying - The index is not stamped to an earlier time point. It is the bam file that is touched and becomes newer than the index (see...

If leaving the original timestamps is not possible, it would be useful if snakemake touched the output files in the order they are listed in output directive, possibly with some...

@melff Thanks for the pointer! I can confirm that `Nelder-Mead` works without warnings. In fact, also `BFGS` works and it is a bit faster. Results vary a bit between the...

...ok I think I made some progress. Admittedly, it's my bad as everything is documented. However, I found the documentation quite terse and I got lost in trying many things....

> The index file is older than the data file Can you make sure the indexes are up-to-date with the bam files? In doubt, you can recreate them with: ```...