Difference: JaysJournal (28 vs. 29)

Line: 1 to 1
	May 2010 archive 06/01/10
Line: 73 to 73
	Start reading up on FM index. 06/03/10
Changed:
< <	Worked on more optimizations, this time guided by Valgrind. From KCacheGrind, I found that about 10-15% of our cycles were being used up in IO, especially making/writing SAM entries. So I went in and did a few more minor optimizations, such as using `ostringstream` instead of `stringstream`. Preliminary results (tested on my machine) shows it runs something like 10% faster now.
> >	Worked on more optimizations, this time guided by Valgrind. From KCacheGrind, I found that about 10-15% of our cycles were being used up in IO, especially making/writing SAM entries. So I went in and did a few more minor optimizations, such as using `ostringstream` instead of `stringstream`. Preliminary results (tested on my machine) shows it runs something like 10% faster now.
	Up until now, I've really only been testing exact matches with saligner over the 125,000 reads file. I was doing one final test on the 2M read file (to verify output and to do a preliminary speed test), I noticed a lot of disk activity after about 40k reads! I'm guessing this is what cache misses look like (it could just be it reading from the reads file, I'm not really sure on this, have to confirm), so I'm going to have to do some more profiling with Callgrind. Granted, my system doesn't have as much memory as `skorpios`, but this might be one of the areas we can improve on.