Speed up depthgauge

[Kekananen]

Is there a way to increase the speed of depthgauge besides setting / increasing threads? When running on ~100 viral samples it takes around a day and a half to complete and seems to run more slowly when the number of samples is increased. In the beginning, it quickly works through the first 50 or so, but then slows to an approximate rate of 1 per ~40mins towards the end of processing the samples.

With having threads set to 4, on ~190 samples it took >3 days to finish running. So the average time expected for calculating the depth of viral samples is around ~40mins per sample.

[jblachly]

probably the python code is very inefficient; should never take that long

[jblachly]

It should take like an hour at most