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

# Which population to plot
species_names = ["Bacteroides_vulgatus_57955"]*6

# Output filename
filename = parse_midas_data.analysis_directory+'example_vulgatus_figure.pdf'
stats_filename = parse_midas_data.analysis_directory+'example_vulgatus_stats_figure.pdf'
output_filename = parse_midas_data.analysis_directory+'example_vulgatus_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
    
    if population_idx>0 and freqs[0:3+population_idx+1].max() < 0.05:
    	condition=True
    elif population_idx==0:
    	condition=((freqs.max()-freqs.min())>=0.8)
    return condition
    
def color_rule_out_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths):
    
    if population_idx>0:
    	condition = not color_rule_in_condition(population_idx, chromosome, location, gene_name, variant_type, times, freqs, depths)
    else:
    	condition = False
    	
    return condition
