Parameterize the logging frequency for ProgressLogger.

[gbggrant]

Make the logging frequency used by the ProgressLogger available as an input. If not used, sets the default value.

Variants team is using a branch of gatk and have made this change there, so pulling this change into master to simplify future merges / branch updates.

[lbergelson]

@gbggrant 👍

I'd really like to merge the asynchronous progress logger that logs every N seconds instead of N records to get around this problem.

[lbergelson]

@gbggrant If you have more PR's into master it would be a good idea to tag someone on engine team. That way they won't get accidentally ignored. I tend to not look at the GVS PRs because I just assume they're being handled by the GVS team.

[gbggrant]

Thanks @lbergelson !