fix view-arg-threads
store some transition terms in log space to avoid infinities
codequality
addition codequality
more calculation simplifications
Merge branch 'master2' into mjh-arg-sample

Conflicts:
	src/trans.cpp
	src/trans.h
adjust indenting for IntervalIterator
use bool for have_mean
change tabs into spaces
indent Tree code
change indent from tabs to spaces
fixed uninitialized variable warning
change snp_infile and infile so they are cleaned up automatically
remove flush commands
fix weird delete statement
removed old commented-out code
use printError() and abort() for error reporting
added some comments to IntervalIterator class
use reference operator in several places suggest by matt
fix node counting from newick tree to ignore parens within brackets