Gene level calls and dual run mode

Merged in pull request #4 from A. Penson which added

• Gene level calling script (get_gene_level_calls.R)
• dual run mode to run with using dipLogR from first
• improved plotting

First release

Merged in upgrades from pensona (no-rerun, pass options from run.sh to doFacets, --ndepth) and mark for the first release to Firework team