uci-cbcl/genomix — pull request #73 by jakebiesinger (2013-11-27 00:26:32+00:00)
Title: add version of tipremove that doesn't require graph compression

@anbangx take a look. This version implements TIP_REMOVE in an uncompressed graph. I'm going to do some timing on it but I thought you'd want to have a look.

There is one slight difference in this version vs. the previous tip remove: since there may be several tip searches in the graph happening simultaneously, the actual behavior is slightly different. One tip can be removed before another tip so the second tip, if longer, may not be removed when in the original it would be. For example:

```
_____C
...A------B<
---------------------D
```
Both C and D would be tip in the compressed graph and would be removed, leaving only `A-----B`. In our case, there's a chance that C will be removed first, which will make D look longer than it did in the compressed graph.