Close the scanning outputStream when we are done with it and propagate the message that the thread is done.
reads-file-stats: remove any path from basename in the output.
Add a timeout for waiting on other threads.
 Expose the default
   sub-sample size with a dynamic option called sub-sample-size in IterateSortedAlignmentsListImpl.
   (-x IterateSortedAlignmentsListImpl:sub-sample-size <int>)