Need a better progress meter for MatchSamples

[kbeutel]

The BufferedWriter sometimes doesn’t write anything for 12+ hours at a time, which makes us think that the algorithm is stuck and hanging. It would be nice to monitor the BufferedWriter and force a write every 1-5 minutes or so. If we’re in a loop, then keep track of the last force write and force write if it if enough time has elapsed.