restructured chiptools function package
updated chiptools data writers to write line by line rather than toString()'ing the whole data object. JProbe now correctly flushes the output writer
updated util Probe class to include information about mutation coordinates
updated util Probe class combine method to combine mutation sites as well.
implementing mutate() method in ProbeUtils for mutating probes to ensure that non binding regions are below a certain escore cutoff
mutate method in ProbeUtils fully implemented. Need to test
updated chiptools Probes data class to color both binding sites and mutation sites using html
renamed Probes html generating functions for clarity
Created chiptools ProbeMutator function. Probes data class appears to display mutations correctly in the GUI. EscoreArgument updated to allow for different default values to be set on construction. There appears to be a bug in the ProbeUtils.mutate() function that allows regions that should be protected from mutations to be mutated. Need to look in to further
rewriting the mutate() function
implemented several helper methods for the new mutate() method.
finished implementing new mutate() method. Appears to work correctly now. Removed old mutate implementation