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Thursday, March 19, 2009

Findpeaks 3.3... continued

Patch, compile, read bug, search code, compile, remember to patch, compile, test, find bug, realized it's the wrong bug, test, compile, test....

Although I really enjoy working on my apps, sometimes a whole day goes by where tons of changes are made, and really I don't feel like I've gotten much done. I suppose it's more of the scale of things left to do, rather than the number of tasks. I've managed to solve a few mysteries and make an impact for some people using the software, but haven't got around to testing the big changes I've been working on for a few days on using different compare mechanisms for FindPeaks.

(One might then ask why I'm blogging instead of doing that testing... and that would be a very good question.)

Some quick ChIP-Seq things on my mind:
  • Samtools: there is a very complete Java/Samtools/Bamtools API that I could be integrating, but after staring at it for a while, I've realized that the complete lack of documentation on how to integrate it is really slowing the effort down. I will proably return to it next week.
  • Compare and Control: It seems people are switching to this paradigm on several other projects - I just need to get the new compare mechanism in, and then integrate it in with the control at the same time. That will provide a really nice method for doing both at once, which is really key for moving forward.
  • Eland "extended" format: I ended up reworking all of the Eland Export file functions today. All of the original files I worked with were pre-sorted and pre-formatted. Unfortunately, that's not how they exist in the real world. I now have updated the sort and separate chromosome functions for eland ext. I haven't done much testing on them, unfortunately, but that's coming up too.
  • Documentation: I'm so far behind - writing one small piece of manual a day seems like a good target - I'll try to hold myself to it. I might catch up by the end of the month, at that pace.
Anyhow, lots of really fun things coming up in this version of FindPeaks... I just have to keep plugging away.

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