PombertLab/SYNY: SYNY-v1.0

Stable release

Changes:

• Fixed abs_path() issue in setup_syny.pl that caused incomplete paths in the output configuration file
• Created check_mp_colors.py to list/plot color palettes available on the system (Fedora 40/Ubuntu 22.04 matplotlib palettes are not the same - 170 vs. 166) + added color palette plot (Images/python_color_palettes.png)
• Added --orientation option for Circos plots to run_syny.pl (possible values: normal, inverted, both) + removed the now obsoleted --no_invert/--no_normal options
• Changed the default Circos plot mode to pairwise (--circos pair); concatenated plots can take a while to compute and are not always useful.
• Circos figures are now plotted in --orientation normal by default instead of both normal/inverted => less wasteful.
• Renamed the .genotype files generated by SYNY as .karyotype to match the nomenclature used by Circos