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

# Which population to plot
species_names = ["Alistipes_finegoldii_56071", "Alistipes_sp_60764", "Alistipes_onderdonkii_55464", "Eubacterium_eligens_61678",  "Phascolarctobacterium_sp_59817", "Bacteroides_coprocola_61586"]
 
# Output filename
filename = parse_midas_data.analysis_directory+'example_figure.pdf'
stats_filename = parse_midas_data.analysis_directory+'example_stats_figure.pdf'
output_filename = parse_midas_data.analysis_directory+'example_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
