Changing to run createIndex (and also thus do the merging steps).
Not doing merge in our multi-genome indexing attempts; it seems like it may be too slow...
Adding an attempt at sort tests.
Attempting to catch mkqs failing
Instrumenting the real function to check its work. Also made a test case but I don't want several gigs of data in my test cases, so it runs on a data file that doesn't trugger the issue.