bugfix for FR merge but w/ performance regression; test cases

@anbangx @Nan-Zhang @JavierJia 
Hey guys,  I officially suck at bit twiddling.  Both FR and RF merges are currently just converting the other kmer to a string.  But! this fixes the indel and SNP problem we saw when doing tests (hooray!)

Any volunteers for going back and fixing this code?  (it's so ugly...)

Anyone? Bueller?