Difference: JaysTermTwoJournal (5 vs. 6)

Revision 62011-01-14 - jayzhang

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META TOPICPARENT	name="NGSAlignerProject"

01/05/2011

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

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To do:

Finish the test driver

Added:

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>

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!

-- Main.jayzhang - 05 Jan 2011

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