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