Difference: JaysJournal (39 vs. 40)

06/18/10

Finally got my code to compile for the C string conversion. Now it's off to fix bugs and segmentation faults! I managed to clear up all the segmentation faults during the actual alignment process, but the output's still not quite right. My new build seems miss most of the reads that are alignable from an old build. Also, I get a segmentation fault during the index building process, which is really strange because I haven't even touched the code for that. No new code is even called until after the index has been built! Maybe I'll have to run the build through the debugger...

I also spent a large portion of the day experimenting with an idea I had last night. When calculating the rank value for a position i, instead of going to the next smallest pre-calculated position and doing popcounts up until i is reached, I modified the function so it goes to the nearest pre-calculated position, and either goes up or down from there. According to callgrind, popcount only gets called about 60% as much on the 125000 read dataset (170,862,051 vs the original 254,181,103 calls). Unfortunately, this only results in a very small speed increase, something like 3-5%, which is strange because I expected the gain to be a lot more.

Edit: Just noticed Daniel's started to implement a different rank structure, so my change might not even be relevant :(.

Finally, I noticed Daniel's made a lot of changes...not looking forward to the huge merge later...

To do:

• Fix bugs in the new C string version.