Updates for plot.map-to-ref.py file

[gregorysprenger]

After running the plot.map-to-ref.py file a few times, here are some suggestions to fix some issues:

• For bottom plot, only show up to 100%
  • Place ax.set_ylim(0, 105) on line 404
• Add .decode('utf-i') to lines containing sys.stderr.write` due to issues with parsing the error outputs
  • If using python > 3.7, sys.stdout.reconfigure(encoding='utf-8') may work instead of the above?
• Change temp directory from /tmp to $HOME/tmp
• Add option to save tmp outputs
• XLSX output fails due to exceeding the number of allowed rows
  • Implement an if statement like: if rows >= X, default to CSV output