Refactor on top of Nan's changes to remove syntax errors

@Nan-Zhang @Elmira88 @anbangx @JavierJia 

These changes are on top of @Nan-Zhang's recent refactoring.  In one fell swoop, Nan:
 - removed the edge readids
 - added `thisReadSequence`, `mateReadSequence`

which effectively obliterates `SplitRepeat` and `Scaffolding`.  This branch is based on Nan's branch and is just the changes to remove syntax errors that were present in his branch.  It's likely that stuff is broken.  Further, with these changes there are several optimizations we can make such as using `Kmer`s (not `VKmer`s) as the `vertexId` and in all the `Node.edges`. I haven't made any of those changes here. Finally, there are places where variable names should be changed (e.g., `edgeMap` doesn't make sense anymore).  I made some changes along those lines where I saw them, but I've likely missed a few.

@anbangx can you look closely at the pregelix-specific code to see if I made any stupid logic errors?

@Elmira88 you should be able to use this branch directly.  I'd suggest you `git cherry-pick` only the exact commits you want applied.  For example:
```bash
$ git checkout <your-current-ray-branch>
$ git log
# record all hashes from the commits you've made for Ray.
# don't include any duplicates and don't include the commit where you merged with Nan's previous code
$ git checkout wbiesing/ray-genomix-refactor  # get these changes
$ git checkout elmira88/implementing-ray  # start a new branch based on this one
# now we will select only the commits you made before and reapply them onto this branch
# for example, say you want to start at commit a65asd6 and include all commits up until f756a7c
# let's call those START_COMMIT and END_COMMIT:
$ git cherry-pick START_COMMIT^..END_COMMIT  # don't forget the ^
$ git log  # notice that everything from START_COMMIT to END_COMMIT has now been applied *on top* of my commits in this branch
# repeat for each range of commits you want to add
```

Let's get the Ray scaffolding in place as soon as we can :v: