Support for coloring of ChEBI Modified Base Codes

[marcus1487]

It is currently possible to select the color for the reserved modified base codes, but all of the other values are lumped into the same "other" color code. At nanopore we are working on the release of modified base callers for inosine and pseudo-uridine. These are both encoded as ChEBI codes and thus display with the same color on IGV. It would be amazing to add support for color codes for specific ChEBI codes. I'm not sure exactly what interface you would use for this, but some type of extendable list with an open text field would seem to make sense. Let me know if some test data would be helpful and I can send over.

[jrobinso]

Test data is always helpful. Otherwise I have to mock it up which takes time.

The "user preferences" windows are limited, by design, hand crafting guis for preferences is not sustainable. This makes the task more difficult than it perhaps should be. But yes we should do it, however we should also add defaults for any codes known to be of interest. You mention 2, we could start with those.

[marcus1487]

I will get you test data shortly. The 3 codes for which we have current or soon to be released models are pseU=17802, inosine=17596 and 4mC=21839. So getting defaults (or at least listing these mods in the preferences panel) would be very helpful in the short term.

[jrobinso]

I can do both for the next point release as a short term stopgap. If you would like to suggest color defaults post them here as rgb strings.

[marcus1487]

There are getting to be too many to have any real meaning. I'd probably just go with the furthest from currently used colors in some logical sense (or start cycling back through the colors). I generally change them to be more aesthetic than the defaults anyways and add legends. Happy with whatever you choose here.

[jrobinso]

Reminder for some test data, when I have it I will add these.