added smc2bed script
added initial versions of arg-summarize.cpp, smc2.bed.cpp, tabix.cpp, tabix.h
some more changes to support arg-summarize
arg-summarize, allow multiple statistics to be extracted concurrently
fixed bug in last commit which caused abort if newick trees requested
small fix, -s option was not recognized as shortcut for --subset
added --recomb option to output (fine-scaled) recomb rates
also added --times to replace branchlengths with exact discrete times
 (so there is no rounding error). But, it currently adds ~30% to run-time
restructure to combine identical regions where no recombination has
occurred between them (this happens in neighboring sample if pruning)-
this is essential for computing recombination rates properly in subtrees.
Also is a starting point for using SPR operations to avoid parsing trees,
potentially speeding up arg-summarize- this is yet to be done but much
easier after these changes.
some fixes from yesterdays update; sample number was not initialized, memory is now freed properly
added SPR operations to tree (including subtrees), speeding up arg-summarize and smc2bed.
correct recomb/coal times with vector of discrete times.
also cleaned up propogate_map (no more special case for root).
added age_diff function to make sure branch lengths are always >= 0.
changed print_newick to print in more consistent order, makes zipping more
efficient.
switch to double for all times, not enough precision otherwise
some bug fixes to SPR/subtree algorithm and arg-summarize
Merge /home/melissa/argweaver.git_bare

Conflicts:
	src/Tree.cpp
	src/Tree.h
update arg-summarize to version 0.2 to reflect SPR improvements
few small changes to prevent memory leaks
Fixed typo where trees ended in colon instead of semi-colon.
Also do not allow recomb_node to be root in subtrees.
do not let recomb_node == coal_node on subtree
now arg-summarize always outputs sorted bed