The interesting thing, to me, is the maturity of the code (in terms of features implemented). In neither cases is it all that great, as it's mostly lacking features I consider to be relatively basic, and relatively naive in terms of algorithms used for peak detection. Though, I suppose I've been working with FindPeaks long enough that nearly everything else will seem relatively basic in comparison.
However, I'll come back to a few more FP related things in a moment. I wanted to jump to another ChIP-Seq related item that I'd noticed this week. The Wold lab merged their Peak Finder software into a larger development package for Genomic and Transcriptome work, which I think they're calling ERANGE. I've long argued that the Peak Finding tools are really just a subset of the whole Illumina tool-set required, and it's nice to see other people doing this.
This is the development model I've been using, though I don't know if the wold lab does exactly the same thing. The high-level organization uses a core library set, core object set, and then FindPeaks and other projects just sit on top, using those shared layers. It's a reasonably efficient model. And, in a blog a while ago, I mentioned that I'd made a huge number of changes to my code after coming across the tool called "Enerjy". I sat down to figure out how many lines were changed in the last two weeks: 26,000+ lines of code, comments and javadoc. That's a startling figure, since my entire code base ( grep -r " " * | wc -l) is only 22,884 lines, of which 15,022 contain semi-colons.
Anyhow, I have several plans for the next couple of days:
- try to get my SVN repository to somewhere other people can work on it as well, and not just restricted to GSC developers.
- Improve the threading I've got going
- Clean up the documentation, where possible
- and work on the Adaptive mode code.
Hopefully, that'll clean things up a bit.
Back to FindPeaks itself, the latest news is that my Application note in Bioinformatics has been accepted. Actually, it was accepted about a week ago, but I'm still waiting to see it in the advanced access section - hopefully it won't be much longer. I also have a textbook chapter on ChIP-Seq coming out relatively soon, (I'm absolutely honoured to have been given that opportunity!) assuming I can get my changes done by Monday.
I don't think that'll be a problem.