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

01/10/2011

Nearly finished the small test driver with a (very) small test set. I realized there's an issue with the hash index that doesn't actually allow me to get a sequence out for the local aligner, only a position, so I'll have to correct that before finishing. Otherwise, the very basic tests look good and it looks like everything is working properly.

To do:

• Finish the test driver

01/13/2011

Finished the test driver, and it looks like it works, even when simulating low memory conditions in the hash index. I tested using a manually generated test sequence + some test reads, and also using the E. coli bacterial genome and both work fine. I decided to add an ExtractString method to the hash index to allow extraction of the string from a position (much like the getPosition method in the FMIndex) to make it all work. I feel like that method could be optimized, but that can be for later.

To do:

• Start a very basic GPU implementation of the aligners!

01/17/2011

Started a new branch for the GPU stuff. I think the first thing I'm going to implement is an "aligner" that just finds how many matches straight-up matches there are. I got the emulators and everything working again, so I have my development environment set up; I forgot to write down what I did last time to get everything to compile and run properly, so I ended up having to re-research it all again, which was a pain. Also started reading through guides and tutorials and taking notes.

To do:

• GPU stuff.

-- Main.jayzhang - 05 Jan 2011