>Well, I’ve finally gotten to it: the tag for FindPeaks 4.0. At this point, I’m more or less satisfied with what made it in to this release: Saturation, Controls, Compares and a whole lot of changes to the underlying machinery. The documentation is still going through some changes, (I have another two flags to add in) and a lot more clarification to do on what some of the parameters actually accomplish, but it’s now in a reasonable state.
Despite the milestone, this project is really a constant evolution. I’m already thinking about what should be in the next version (4.1?): Support for SAM/BAM, “peakless peak calling” for regions instead of peaks, a vastly upgraded FindFeatures code and a host of small changes that I had thought weren’t worth the effort for this particular release. I’m even considering a GUI, if I can squeeze it in. (If anyone would like to help out on that project, I’d be thrilled to add them to the project!)
At this point, I’m happy to say I’m not aware of any outstanding coding bugs – although I do take it seriously that there is an open bug remarking that the documentation is insufficient. I’ve been worknig on improving it, and reorganizing the manual, which should be done in the next couple days. Once that’s done, I’ll jump back into using my code to do some analysis of my own. There are a few really neat things, based on work on my poster, that I’d like to play with. I guess that’s what they say about coders: when you write software for yourself, you never lack the motivation to add in one more feature. (=