While the Gene Indexer can be "automated", it does not do so well, smoothly, or without needing constant babying to make sure that it's still working... It has three issues that prevent easy, will-not-randomly-break, automation:
- Indexer does not Auto-Eject 100% gene samples. The biggest issue with the Indexer is that it will fill up rather quickly and stop working. This happens for multiple reasons, the simplest of which to fix is that the indexer does not auto export 100% gene samples on it's own. This is very important, as not only does this require NBT item filtering, which not many item transport mods support, but there are a LOT of bee genes, and setting up NBT filters for every single gene isn't just a time consuming hassle, but a logistic challenge/nightmare if your item transport system doesn't support near infinite filter settings, meaning you have to try and figure out a way to use multiple import AND export connections on a single block (as far as I know, only Pipez allows for unlimited filter settings, but requiring a specific mod for your mod to work, outside of a library, is poor design - I've also had my Pipez filters randomly disappear, forcing me to redo hundreds of filter setting for this one block)! Having the Indexer itself push out 100% gene items would not only solve how to get them, and only them, out of the Indexer, but also keep said indexer from filling up and thus no longer working.
- Indexer only combines genes when not stacked. Two "Passive 1%" genes will stack, and any automation setup will send them as a stack into the Indexer, but the Indexer can only work on them if they are placed in separate slots in the Indexer. This leads to yet more space wasting in the Indexer, as now to combine any one gene you need three slots, 1 for the 100%, 1 for a stack of identical 1-4% genes, and a third slot for the first same gene type that won't stack with the current gene stack. This means that the Indexer could wind up filled with stacks of 2-4% genes, which could have been combined into at least one 100% gene, but which didn't because the Indexer doesn't work properly. Either the code needs to be recalibrated to notice when genes are stacking, or there should be an invisible inventory that all genes first go into, from which they are dolled out one item at a time into the Indexer's actual gene combining inventory.
- The Indexer's inventory is too small. Even with the two aforementioned improvements, it's still to small to handle being given all possible bee genes and actually working. It needs to be massively expanded so that it's at least pseudo infinite. Ata bare minimum, if there was a separate (invisible?) inventory for filled genes from which they get auto exported into a nearby chest or pipe, and another (invisible?) inventory where any genes imported into the Indexer (via GUI or pipes) gets added and combined, the main inventory of combined pre-100% genes still needs to be at least 512 slots big, to ensure that even with a mod pack like ATM and added bees, there will always be enough inventory slots for every gene type (see sophisticated storage for how to make a GUI for an inventory that big - a search bar would be a good idea).
While the Gene Indexer can be "automated", it does not do so well, smoothly, or without needing constant babying to make sure that it's still working... It has three issues that prevent easy, will-not-randomly-break, automation: