Parameters.toml

#This is an example of parameters files of dynamic

[[Graph]]
row = 25
col = 25
dim = 3
N_starting_cells = 1
# ***
# Otherwise matrix adjacency
# ***#
matrix_adjacency = "./utility/Example_adj_matrix.txt"

[[Dynamic]]
Model = "contact"
Max_time = 1000.0
rate_birth = 0.2
rate_death = 0.01
rate_migration = 0.01
drive_mut_rate = 0.01
average_driver_mut_rate = 0.4
std_driver_mut_rate = 0.1
t_bottleneck = [50.0,150.0]
ratio_bottleneck = [0.8,0.8]
[[Sampling]]
Random_sampling = 1
num_cell = 10
#***
# If Random_sampling = 0
# ***#
pos_center = 0
radius_sampling = 10

[[MolecularEvolution]]
length_genome = 6000
prob_base = [0.3,0.2,0.2] #only A,C,G

type_isa = 0

#*** if type_isa = 1 ***#
neut_mut_rate = 0.000025

#*** if type_isa = 0 ***#
approx_snv_indel = 1
sub_model = "K80"
indel_size = 300
lavalette_par = 0.5
indel_rate = 0.0
params = [{"alpha" = 0.5, "beta" = 0.3}]

#*** if signature ***#
mut_rate_avg = 0.000001
used_sign = ["SBS1","SBS4","SBS16"]
vector_change_points = [0.0,50.0]
vector_activities = [[0.7,0.2,0.1],[0.0,0.3,0.7]]
ratio_background_signature = 0.000001

[[BulkExperiment]]
coverage = 10.0
FP = 0.000005
FN = 0.000002

[[ART]]
command = ""
#*** Otherwise write paramaters ***#
profile = "HS25"
len_read = 150
tot_num_reads = 10
outfile_prefix = "example"

paired_end = 0
#*** if paired_end == 1, they are require **#
mean_fragsize = 200
std_fragsize = 10

mate_pair = 0