Difference: JaysJournal (5 vs. 6)

Revision 62010-05-12 - jayzhang

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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:

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Read up on CMake a bit more; it's still giving me a strange amount of trouble...

05/11/10

Changed:

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Today felt pretty pointless. I managed to finish my score-only Smith-Waterman alignment, but it ended up failing a bunch of tests. So I took a look at the SHRiMP code again and made a few changes based on that code to iron out the bugs. In the end, my code ended up looking almost exactly like the SHRiMP code, and yet was still buggy, so I ended up just copying and pasting the code into my version. I decided to cut and paste the SHRiMP code into my own class for a couple of reasons:

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I'll have to use that code again, but modified when I do the full alignment (with traceback).

Changed:

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The SHRiMP code required a call to initialization, which was troublesome and not really required given the way the NGSA LocalAligner works.

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The SHRiMP code required a call to initialization, which was troublesome and not really required given the way the NGSA LocalAligner works.

Since SHRiMP was in C, I couldn't wrap their functions in namespaces.

I'll still have to make sure if my decision was correct with Chris, though.

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