This helper function calculates the start and end index for each character in the BWT.  Basically, the information
        generated here is for quickly finding offsets.  This is run AFTER self.constructTotalCounts(...)

def constructIndexing(self):
        '''
        This helper function calculates the start and end index for each character in the BWT.  Basically, the information
        generated here is for quickly finding offsets.  This is run AFTER self.constructTotalCounts(...)
        '''
        #mark starts and ends of key elements
        self.startIndex = [None]*self.vcLen
        self.endIndex = [None]*self.vcLen
        pos = 0
        
        #go through the 1-mers
        for c in xrange(0, self.vcLen):
            #build start and end indexes
            self.startIndex[c] = pos
            pos += self.totalCounts[c]
            self.endIndex[c] = pos