-
Notifications
You must be signed in to change notification settings - Fork 0
/
config.ini
116 lines (96 loc) · 2.37 KB
/
config.ini
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
[main]
output_level = 2
random_walk = no
loop_density = 5
use_2D = no
max_pet_length = 1000000
long_pet_power = 2.0
long_pet_scale = 1.0
steps_lvl1 = 1
steps_lvl2 = 1
steps_arcs = 1
steps_smooth = 1
noise_lvl1 = 0.5
noise_lvl2 = 0.5
noise_arcs = 0.01
noise_smooth = 5.0
[cuda]
num_threads = 512
blocks_multiplier = 16
milestone_fails = 3
[data]
data_dir = ../data_GM12878/
anchors = GM12878_anchors.bed
clusters = GM12878_clusters.bedpe
factors = CTCF
singletons = GM12878_singletons.bedpe
split_singleton_files_by_chr = no
singletons_inter = mock.txt
segment_split = ../data_GM12878/GM12878_segments.bed
centromeres = ../data_GM12878/hg38.bed
[distance]
genomic_dist_power = 0.75
genomic_dist_scale = 0.5
genomic_dist_base = 1.0
# singletons interaction frequency to 3d distance (segment level)
freq_dist_scale = 25.0
freq_dist_power = -0.6
# interchromosomal singletons interaction frequency to 3d distance (chromosome level)
freq_dist_scale_inter = 120.0
freq_dist_power_inter = -1.0
count_dist_a = 0.2
count_dist_scale = 1.8
count_dist_shift = 8
count_dist_base_level = 0.2
[template]
#template_segment = ...
template_scale = 7.0
#dist_heatmap = ...
dist_heatmap_scale = 15.0
[motif_orientation]
use_motif_orientation = no
weight = 50.0
[anchor_heatmap]
use_anchor_heatmap = no
heatmap_influence = 0.5
[subanchor_heatmap]
use_subanchor_heatmap = no
estimate_distances_steps = 4
estimate_distances_replicates = 4
heatmap_influence = 0.1
heatmap_dist_weight = 0.01
[heatmaps]
inter_scaling = 1.0
distance_heatmap_stretching = 2.5
[springs]
stretch_constant = 0.1
squeeze_constant = 0.1
angular_constant = 0.1
stretch_constant_arcs = 1.0
squeeze_constant_arcs = 1.0
[simulation_heatmap]
max_temp_heatmap = 5.0
delta_temp_heatmap = 0.9999
jump_temp_scale_heatmap = 50.0
jump_temp_coef_heatmap = 20.0
stop_condition_improvement_threshold_heatmap = 0.99
stop_condition_successes_threshold_heatmap = 10
stop_condition_steps_heatmap = 50000
[simulation_arcs]
max_temp = 5.0
jump_temp_scale = 50.0
jump_temp_coef = 20.0
delta_temp = 0.9999
stop_condition_improvement_threshold = 0.975
stop_condition_successes_threshold = 100
stop_condition_steps = 50000
[simulation_arcs_smooth]
dist_weight = 1.0
angle_weight = 1.0
max_temp = 5.0
jump_temp_scale = 50.0
jump_temp_coef = 20.0
delta_temp = 0.9999
stop_condition_improvement_threshold = 0.99
stop_condition_successes_threshold = 50
stop_condition_steps = 50000