uci-cbcl/genomix — pull request #89 by anbangx (2013-12-06 20:10:41+00:00)
Title: Anbangx/add bubble merge statistics

@jakebiesinger @JavierJia @Nan-Zhang @Elmira88

This PR provides statistics counters and log information for bubble merge.

For statistics counters, you can see the distribution histograms by specifying command line option -runAllStats. Distribution histograms include totalPaths, removedPaths, editDistance, fractionDissimilar, totalPathsCoverage and removedPathsCoverage.

For log information, you can get all relative information of bubbles.
Ex. A and B are two paths to form bubble, C and D are the major and minor of AB bubble respectively.
LOG:
Major: C Minor: D
numOfPaths: 2
No.1 bubble(internalKmer): A PathLength: ... Coverage: .. ID: ...
Dissimilar: .... with B bubble
No.2 bubble(internalKmer): B PathLength: ... Coverage: .. ID: ...
Dissimilar: .... with A bubble
Remove # bubbles: No.2 bubble - A;
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////

I merged with our current branch. Jake just updated MaxLength for bubble. I run it on ecoli dataset in hpc. You can check the log under ~anbangx/workerlog and the distribution histograms under /cbcl/anbangx/output/bubble-stats/01-BUBBLE-STATS/counters.