CAFE underflow

[benfulton]

Does the max_size option or the filter command keep track of which families are left out of the analysis? I think the reason I don't use the filter command is that it doesn't tell me which families were filtered out.
It's not that important for the filter command, but for max_size, what I typically do is remove families greater than max size, estimate lambda, and then go back and use the estimated lambda to reconstruct gene counts for the families that were over the max size. So I think it would be nice if max_size did that as well!

[gwct]

I don't think either command lets the user know which families are being filtered. I don't use the max_size command, but I agree that it would be a nice feature for the filter command if CAFE wrote two files: one with the actual families used in the analysis in CAFE's input format (so that file can just be used again) and one file listing the families removed.