Give life to the --target-regions option.
Extract pre-execution parameter validation to its own method
Other comments/code in execute() indicate this param is deprecated
Call the method instead of remembering the value
extract method for the start log message
extract method for creating the variant reader iterator
extract method to set up the report/output filehandle
remove unused variable
extract method to close the report filehandle

the temp_output_file name needs to be saved between the call to
_setup_report_fh and _close_report_fh
build param checking moved into validation method
Move the data caching check into the validation method

Also removed the now-useless benchmaking around the now-removed caching
remove useless benchmarking around annotation setup

There's nothing to benchmark other than the time to open the variant
input file.  If we want to add instrumentation to that, then we'll
add it in later
extract method to create the annotator object
extract method for the main annotation loop
lc() and validate the annotation_filter param in the validate method
simplify delegating to the appropriate annotator method
improve efficiency when accept_reference_IUB_codes is in use

Validate the option once in the validator method

Create a sub to transform the reference once before the annotator loop starts
and call it in the loop.
avoid a 'used once' warning
Merge remote-tracking branch upstream/$:{upbranch}