Adam Taranto

Adding symlinks to the programs in the `BandageNG.app/MacOS` dir alongside the BandageNG app does not work. It would be useful to have an option to enter a custom PATH in...

I found the [GFA tag name](https://github.com/asl/BandageNG/wiki/Custom-GFA-tags#node-depths) info on your wiki. I'll add a slightly different question: If I have a BED file with coverage information for windows across a contig,...

Re depth tags: Unicycler seems to use `dp` as a depth tag instead of `DP` so is not picked up by BandageNG. This can be fixed with: `sed -i 's/dp:f/DP:f/g'...

Seeing as unicycler produced assemblies with `dp`, could you add that as a depth option? Apparently, lowercase `dp` is used as it is not standardized in the GFA spec: [see...

@tanghaibao where is the code that computes the correlation and flips the annotations that you mentioned above? I've implemented a manual flip feature in my dev fork that would handle...

Ok cool, so `get_orientation()` decides if one of the sets of genes needs to be flipped. Where do you calculate the new flipped coords for genes on a flipped chrm...

I have a development branch that works for this. It is currently undocumented and you will need to provide your own alignments. I can provide some support if you want...

I was using Jupyter Notebook* to edit nbgrader notebooks without issue a few months ago. Is there a new version of Jupyter that has caused the old UI not to...

The nbgrader options used to be at the [top of each cell like this](https://youtu.be/5WUm0QuJdFw?t=515). It now has this [weird sidebar thing](https://github.com/jupyter/nbgrader/blob/main/nbgrader/docs/source/user_guide/images/creating_assignment.gif).

Sorry, I meant to say that Jupyter Notebook has switched from cell toolbar to the sidebar. Jupyter Lab used the sidebar in old versions as well. I've edited my question....