Default output should not be so verbose

[SichongP]

By default the tool prints A LOT of unnecessary messages. When using -n, every thread reports the same logging messages repeatedly. Most of the warning messages like skipping alignment steps, references used, etc can and should only be printed once (if at all) since there is no reason for each thread to have different conditions.

Additionally, it should only report major progress + any program-crashing error messages. All other information can be printed to a log file instead of stdout, unless user specifically asks for it (with --verbose).

I know this problem can be easily avoided by redirecting but it can be a bit of a shock for any unsuspecting new users. I had my jupyter window completely frozen by the huge dump of output. Redirecting is also not ideal since you'd still want to alert users with some critical information.

I'd be happy to implement a logger and send a PR if this is desired.

[Magdoll]

Hi @SichongP ,

Duly noted. If you want to implement a logger please go ahead and do a PR. It isn't super high on my priority list...
-Liz