######################################################
#
# Make a copy of this file and edit it to your liking
#
######################################################

# Which population to plot
species_names = ["Bacteroides_vulgatus_57955", "Bacteroides_uniformis_57318", "Bacteroides_cellulosilyticus_58046", "Roseburia_inulinivorans_61943", "Bacteroides_stercoris_56735",  "Bacteroides_caccae_53434"]
  
# Output filename
filename = parse_midas_data.analysis_directory+'debug_figure.pdf'
stats_filename = parse_midas_data.analysis_directory+'debug_stats_figure.pdf'
output_filename = parse_midas_data.analysis_directory+'debug_figure_snps.txt'

####################################################################
#
#  Function controlling which mutations are colored
#
#      Returns: true for colored
#               false for not colored
#
####################################################################
def color_rule_in_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    condition = False
    
    return condition
    
def color_rule_out_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    condition = False
    
    return condition
