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

# Which population to plot
species_names = ["Bacteroides_uniformis_57318", "Bacteroides_massiliensis_44749", "Bacteroides_cellulosilyticus_58046"]
 
 
# Output filename
filename = parse_midas_data.analysis_directory+'boring_bacteroides_figure.png'
output_filename = parse_midas_data.analysis_directory+'boring_bacteroides_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
    
    #condition = not ((freqs<0.2).all() or (freqs>0.8).all())
    condition = (freqs.max()-freqs.min())>0.3
    
    return condition
    
def color_rule_out_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    condition = False
    condition = len(freqs)<10
    
    return condition
