Trying to pin down the sketchy bug with more debugging. It looks like the C++ code is just lying about the first position for left-mapping sometimes.
Fixing hadoop-bam version.
Also indexGenome changes, because it still doesn't use arguments
Not passing phantom nodes at the wrong end of generalization edges to the next MergingScheme. Also dummid in the NonSymmetric merging scheme
Finding corresponding representatives from pairs of sets of Sides to merge, to properly support merging when building the next level Sides. Still need to handle de-duplicating edges.
Should be able to properly de-duplicate edges now. No idea how to write a test case for that.
Merge branch 'master' of bitbucket.org:adam_novak/sequence-graphs