CHANGES.txt

v0.1.2, June 23, 2023 -- Output files are more consistent in formatting
                         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
v0.1.1, July 13, 2021 -- Fixed bug when not specifying partition
v0.1.0, June 25, 2021 -- Initial release