reworked tree time to treeTime2 parallel not really much speed up over
serial version.....
added a new hap class that just holds population information
	maps pop index 2 name
	maps pop index 2 sample size

	This will be used to construct our node by snp array
Started an over haul of the way mutation is carried out
	First we start by making a "matrix" that is nodes by totalSnps
	Then we fill it with 2s From here we sprinkle in our mutations
	then for each node containing a mutation change the 2 to a 1
Huge reworking of the way that mutations are added to our coalescent
trees. Using a single array and now mutation is done in parallel. Also
writing of data files is done in "parallel" at least each file is
concurrently written in seperate threads.
now take into account more param files and log
Hopefully fixed some casting errors and made the nodes * nodes -1 into
longs so that they can be multiplied.
idum should have been a reference to a pointer ie it should have changed
on each call to ran2 but it was set at the abs(seed) so that should be
in working order now.
		Still have ran2 concurrency issues...
made randomDouble() synchronized because of threading.
added some timing stuff but who knows how accurate they really are?
Changed the mutation array to byte from int to save on memory should be about a 3/4 less memory consumption?
Added a way to pass an argument to set the parallelism. Use the -proc