This function constructs the total count for each valid character in the array or loads them if they already exist.
        These will always be stored in '<DIR>/totalCounts.p', a pickled file

def constructTotalCounts(self, logger):
        '''
        This function constructs the total count for each valid character in the array or loads them if they already exist.
        These will always be stored in '<DIR>/totalCounts.p', a pickled file
        '''
        self.totalSize = self.bwt.shape[0]
        
        abtFN = self.dirName+'/totalCounts.p'
        if os.path.exists(abtFN):
            fp = open(abtFN, 'r')
            self.totalCounts = pickle.load(fp)
            fp.close()
        else:
            chunkSize = 2**20
            if logger != None:
                logger.info('First time calculation of \'%s\'' % abtFN)
            
            #figure out the counts using the standard counting techniques, one chunk at a time
            self.totalCounts = [0]*self.vcLen
            i = 0
            while i*chunkSize < self.bwt.shape[0]:
                self.totalCounts = np.add(self.totalCounts, np.bincount(self.bwt[i*chunkSize:(i+1)*chunkSize], minlength=self.vcLen))
                i += 1
            
            #save the total count to '<DIR>/totalCounts.p'
            fp = open(abtFN, 'w+')
            pickle.dump(self.totalCounts, fp)
            fp.close()