Log fixes

Remove the out_dir and log_verbose arguments replace them with a single log=”filename.txt” argument. This will be more explicit, more R-ish (definitely “ish”), and avoid unintended overwrites of previous log files.

The log has a lot of redundancy per record, “TOTAL GROUPS”, “MODEL”, “METHOD”, “CDR3” are identical for each log record. You can put them in the summarized clone object as slots instead (analogous to the distinction between the processing log and console log in presto/changeo).

You can remove the start and end bits from the log:

PREPARE DB>

CLONING> DONE. 
SUMMARY CLONES> ... 
SUMMARY CLONES> DONE.

ParseLog isn’t going to be able to handle them and they are unnecessary.

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