Difference: JaysJournal (10 vs. 11)

Revision 112010-05-18 - jayzhang

Line: 1 to 1

META TOPICPARENT	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:

Line: 90 to 90

Polish up all the code I've written and merge.
Add in my improvements to the original local aligner.

Added:

>
>

05/17/10

I've integrated all the different aligners I've made together into one package. So now, there are two different local aligners, banded and un-banded, each of which have two different implementations, vectorized and non-vectorized. Which version of those two aligners are compiled depends on whether the target machine supports at least SSE2. I haven't really figured out how to get CMake to automatically detect whether SSE2 is supported or not, but instead I've added a variable to the CMakeLists.txt to be set manually.

I also cleaned up my implementations and optimized the existing local aligner implementation (only the ScoreOnlyAlignment method) to be more memory-efficient and faster. All public interfaces for both vectorized/non-vectorized versions of the aligners now match in both input and output and should be more-or-less equivalent in usage (with the exception of the free gap bits in the regular local aligner).

I'm not really sure what else to do for now, so I'll probably have to ask Chris/Daniel tomorrow.

View topic | History: r73 < r72 < r71 < r70 | More topic actions...