(r4) JaysTermTwoJournal < BETA

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---+++01/05/2011
Started reading more in-depth into CUDA. Made some notes (I'll post them later).

Things to do:
   * Finish up the local aligner changes and commit
   * Create a small test driver that ties together the aligners and the has index to verify correctness.

---+++01/06/2011
Finished redoing the banded local aligner. Now I just have to add =FullAlignment= methods into the vectorized aligners. Note that only the =ScoreOnlyMax= methods of the vectorized aligners actually are vectorized. The =FullAlignment= method is just a straight copy from the corresponding non-vectorized aligners, since =FullAlignment= is used much less.

Also, I took out all the kmer index/mapper stuff, since it was still using the old aligner and I didn't want to update it. Those files are really old anyway, and really haven't been updated much for a long time...

To do:
   * Create a small test driver
   * Add =FullAlignment= methods into the vectorized aligners.

---+++01/07/2011
Finished adding in full alignment methods into the vectorized aligners. Now all the aligners are completely redone and I just have to do up the test driver.

To do:
   * Create a small test driver

-- Main.jayzhang - 05 Jan 2011
Topic revision: r4 - 2011-01-10 - jayzhang