05/06/10

I'm starting this journal 3 days late (whoops). Here's a brief overview of what happened during my first three days:

• Read through a bunch of Daniel's journal entries to get myself a little more familiar with the project so far.
• Had a meeting with Daniel and Chris where we discussed my first task:
  • First, I should make or beef up the existing test suite.
  • Then, I'm to make a vectorized version of the Smith-Waterman aligner that Daniel has working.
  • I should also familiarize myself with existing tools (e.g. Bowtie, BWA, Mosaik, and SamTools).
• I ended up spending a lot of time reading through the various guides Daniel posted, as well as the Git guide and the Google C++ style guide to get myself more familiarized with what I should be doing and how I should be doing it.
• I also spent some time reading up on the Smith-Waterman algorithm and reading up on sequence alignment in general to get myself a little more familiar with the project.
• Checked out Daniel's existing code, especially local_aligner.cc bit (which I'm assuming my vectorized SW will be based a lot off of). I can understand the majority of the code, although I'm a little iffy on some of the gap penalty calculations.

So after all that, I think I'm finally ready to do a little coding. Today, I'll mostly be working on the test suite and trying to get that out of the way.

End-of-the-day post:

I've looked through the local aligner source code in a bit more detail and I think I know my way around it pretty well now. I'm still a little unclear on the free gap policies (I understand the premise and a little of how it works, but I still need to wrap my head around some of the cases in the algorithm), but Chris told me not to worry too much about it, as it's not a priority for now.

I've managed to modify Daniel's test/correctness_test.cc so that it works on the existing code, and all the test cases pass. The test cases Daniel wrote were pretty complete but only tested the ScoreOnlyAlignment method in the local aligner. So next up will be writing some test cases for the FullAlignment, which may be a little harder since it doesn't just output numbers. I've written a few tests so far, and I think I may have found one or two bugs (but I'm going to have to look into that some more to see if it was my test case or the code that was failing). So tomorrow, I will mostly be doing...

• Finishing up the test cases for the FullAlignment method.
• Fixing any bugs that might come up along the way.
• If I get a chance...maybe even start looking into the vectorized methods!