Credible shift set now returns all component of class bammdata to facilitate backwards conversion: class credibleshiftset -> bammdata
new R function: getBestShiftConfiguration to get MAP shift configuration
minor changes to addBAMMshifts.R
summary.bammdata.R no longer computing maximum cred shift config
minor change to summary.bammdata
Update R documentation to reflect code changes to BAMMtools
Minor changes to R code