Add an option to only plot somatic mutations

[mfoll]

linked to #73

[mfoll]

Rename the --no_plot option to plot with three possible values:

• all that will produce plots for all variants (the current default behaviour). This will be the default value when the --pairs_file is not provided.
• somatic that will only do the plot when a somatic variant is detected. This will be the default value when the --pairs_file is provided.
• none that will not produce any plot. This will replace the --no_plot flag.