veg/hyphy — pull request #70 by nlhepler (2012-02-19 20:15:43+00:00)
Title: Huge omnibus alignment changes

PLEASE REVIEW, DO NOT MERGE

The vast bulk of these changes are massive refactoring and reworking of alignment code, and most specifically codon alignment. Code has been commented, variables renamed, yadda yadda, all in the hope of readability and grokkability in the future.

Again, DO NOT MERGE

I plan on working with Steven some to develop some testcases for this code, so we know it's working as designed.

Because I've been lax in pushing changes upstream, there are also a few MPI-related fixes, a change to make HyPhy less verbose in production builds, and a removal of a build file. I've been carrying these around for a while -- they're currently at work on the cluster.