Fixing index range vector endpoint, which lets left and right mapping to merged level at least produce something of the right shape
Removed a basedness correction that just seemed to be causing problems
Removing a test that shouldn't actually be true.
Removing some debug prints
Dumping mappings. Something is wrong with the way I am getting my mappings. I need to port the scala mapping code down here.
Re-writing range counter since it was completely wrong. Also suppressing left-mapping.
Adding more Scala tests to try to work out what's going on, but Scala tests don't see this strange lack of 0s in the range vector.
Dumping more of the mask and ranges vectors. I think the problem is that masked-out things are breaking up what my algorithms want to be single ranges.
Stopping masked-out stuff from breaking ranges
Seems to be able to map sequences the right way around now. I was not taking into account orientation corectly when converting from contig, base, face to text, offset coordinates. Maybe we should just standardize on one of those?
Removing extra debug stuff (again). I would add a debug on/off macro, but that's ugly and also there are many meanings of debug
Switching to greedy scheme for MHC test case.
Actually removing those debug prints I thought I removed previously
Making refmhc genome 0 for the greedy merge.
Don't pre-scan the bases for each range from every single thread.