/**
* Parse the -cov arguments and create a list of covariates to be used here
* Based on the covariates' estimates for initial capacity allocate the data hashmap
*/
public void initialize() {
baq = new BAQ(BAQGOP); // setup the BAQ object with the provided gap open penalty
if (RAC.FORCE_PLATFORM != null)
RAC.DEFAULT_PLATFORM = RAC.FORCE_PLATFORM;
if (RAC.knownSites.isEmpty() && !RAC.RUN_WITHOUT_DBSNP) // Warn the user if no dbSNP file or other variant mask was specified