Fixed bug causing chromosomes to not print correctly in "pairwiseMetrics" file
Fixed bug causing state numbers to be printed rather than names in "pairwiseMetrics" file
Greatest hits now only shows significant loci if using null distribution
Greatest hits merging no longer uses 1000 loci when there are < 1000 significant loci
Fixed a bug where epilogos would throw an error if there were no significant loci
Fixed a bug where one diagnostic figure was not showing
Added option to control whether p-values are generated or not (null-distribution)
Changed the exemplar generation approach to find the optimal region using filter-regions maxmean algorithm (see paper)
Added option to control exemplar region width
Added option to control group size in pairwise epilogos
Changed greatestHits/exemplars language to regions of interest/roi
Changed pairwiseVisual.py to roiAndVisualPairwise.py
Changed greatestHits.py to roiSingle.py
Added similaritySearch.py (CL accessible with simsearch)
Added plotRegion.py (Cl accessible with plotregion)
Added -n/--null-distribution flag for controlling p-value generation
Added -w/--roi-width flag for controlling size of generate regions of interest
Added flags for controlling SLURM memory requests
Moved findSign to helpers
Added orderChromosomes function to helpers to determine ordering of chromosomes
Added memory control flags to epilogos
Epilogos no longer defaults to using all memory and cores on a SLURM node
Epilogos no longer only outputs 200bp bins in scores files
Fixed bug where S2 expected was containing negative values
Added flag to control output filenames