input: stream alignment and show progress bar

[ktmeaton]

When working with large datasets (VirusSeq) it would be nice to monitor progress. We could also use multithreading for it (I think), if we don't mind the output being in a different order from the input.

[ktmeaton]

Since reading a file is inherently a linear operation, multi-threading won't be appropriate there. But potentially we can stream the file reading directly into the recombination search, with par_bridge:
https://morestina.net/blog/1432/parallel-stream-processing-with-rayon#Stream_processing