manual integration tests passed
added examples to documentation
modified top20hists function (shows dist of mutations across gene coordinates
fixed combineAberrationTypes2, making the combination and ultimately overlap analysis work on individual patients when it the drug screen and aberration patients come from the same cohort
fixed documentation/example to clear r cmd check
added diagnostic save to get path summary runner out
fixed up image saving and plot handling
fixed issue where combine aberration types was not adding aberration data when cohort was matched and had no coverage limitation
fixed variable naming buggs and documentation