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name="NGSAlignerProject" |
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: |
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- Take a look at the banded Smith-Waterman function and try integrating that, too, perhaps. This function only checks a "strip" of cells going down the diagonal of the score matrix, since in practice, alignments aren't as useful when there are large variations from a full match.
- Finally, in the distant future, start thinking about the free gap algorithms and vectorizing them.
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> | 05/10/10
I spent the morning trying to integrate the SHRiMP vectorized Smith-Waterman code into a new local aligner class, but I couldn't get it to pass the test cases and kept getting segmentation faults, etc. So, I decided it was more trouble than it was worth and to try building my own version of the vectorized Smith-Waterman directly. I also had a lot of trouble getting CMake to do the right thing, but I later figured out it was because I forgot to use the -msse2 -msse3 compiler flags.
I'm about a quarter complete on a score-only vectorized version for the local aligner, and I've got a basic game plan laid out for completing it; I've also found that the best way to understand some code is to try to code it yourself! I now have a much firmer grasp on the whole SHRiMP aligner and on why it does some of the things it does (for example, one question I had was why it stored values for b_gap, but no a_gap array). I think by tomorrow, I can:
- Get the score-only vectorized Smith-Waterman finished and hopefully tested out.
- Time permitting, get started on the full alignment with traceback.
- Read up on CMake a bit more; it's still giving me a strange amount of trouble...
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