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
rename n to node
use old getTreePostNodes function
change private to protected
change sprintf to snprintf
small math simplifation