trying to get the dependencies right
regenerated vignettes with correct dependencies
removed the function get_overlap_counts that is no longer used, analysis now uses the "coverage" function
deleted the documentation for package and the get_overlap_counts function
documenting the missing parameter to bootstrap correlation
documenting missing parameter strand in convert_to_counted
changing similarity_function to similarity to work properly
updated documentation generated
Merge branch 'master' of https://github.com/rmflight/fmcorrelationbreastcaparp1