Added files for z-algorithm computation. Created method templates for one additional alignment filter
Added unit tests for z-algorithm prefix and suffix methods
Completed method to check for maximal matching suffixes and prefixes. Added preliminary unit tests for this function
Added command line options for maximal prefix/suffix read filter
Modified the allelotyper to use the prefix/suffix filter, if requested
Fixed major Z-algorithm bug which caused it to fail on strings of unequal length.
Added functionality to count the number of reads filtered out by each filter. Statistics are printed at the end of allelotyping to the stats file
Fixed bug in which filter stats were printed for every sample. Added unfiltered filter type
Formatted filter stats in allelotype.stats output
Cleaned up namespaces in various header files
Optimized prefix/suffix filter so that it only calculates the values for the reference sequence region of interest
Added function documentation and integer casts to removed signed-unsigned comparison warnings
Added documentation for FilterCounter class
Merge pull request #31 from tfwillems/master

New Alignment Filter
adding experimental scripts directory
fixing noise model PDF scaling
Need to load index for training allelotype model to use alignment filters from twillems. Also fixed uninitialized noise model variables
added quiet flag to turn of messages
tweaking alignment params for massive speedup
fixing phantom STR problem.