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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
A
abs_contact_2_coo_file() (in module instagraal.pyramid_sparse)
apply_replay_simu() (instagraal.cuda_lib_gl_single.sampler method)
approx_all_likelihood_on_zeros() (instagraal.cuda_lib_gl_single.sampler method)
approx_single_likelihood_on_zeros() (instagraal.cuda_lib_gl_single.sampler method)
approx_single_likelihood_on_zeros_mut() (instagraal.cuda_lib_gl_single.sampler method)
approx_single_likelihood_on_zeros_nuisance() (instagraal.cuda_lib_gl_single.sampler method)
B
basic_fragment (class in instagraal.fragment)
blacklist_contig() (instagraal.simu_single.simulation method)
bomb_the_genome() (instagraal.cuda_lib_gl_single.sampler method)
build() (in module instagraal.pyramid_sparse)
build_and_filter() (in module instagraal.pyramid_sparse)
build_frag_dictionnary() (instagraal.pyramid_sparse.pyramid method)
build_seq_per_bin() (instagraal.pyramid_sparse.level method)
C
calc_cov_x() (in module instagraal.leastsqbound)
close() (instagraal.pyramid_sparse.pyramid method)
copy() (instagraal.fragment.fragment class method)
copy_from_gpu() (instagraal.gpustruct.GPUStruct method)
copy_to_gpu() (instagraal.gpustruct.GPUStruct method)
create_gpu_struct() (instagraal.cuda_lib_gl_single.sampler method)
create_new_sub_frags() (instagraal.simu_single.simulation method)
create_sub_frags() (instagraal.simu_single.simulation method)
cuda_gl_init() (instagraal.instagraal.window method)
D
debug_test_EM() (instagraal.instagraal.window method)
debug_test_model() (instagraal.instagraal.window method)
define_inter_chrom_coord() (instagraal.pyramid_sparse.level method)
discard_low_coverage_frags() (instagraal.simu_single.simulation method)
display_current_matrix() (instagraal.cuda_lib_gl_single.sampler method)
dist_inter_genome() (instagraal.cuda_lib_gl_single.sampler method)
draw() (instagraal.instagraal.window method)
draw_axes() (in module instagraal.glutil)
draw_line() (in module instagraal.glutil)
E
err() (in module instagraal.leastsqbound)
estimate_max_dist_intra() (in module instagraal.init_nuisance)
(in module instagraal.optim_rippe_curve_update)
estimate_max_dist_intra_nuis() (in module instagraal.optim_rippe_curve_update)
estimate_param_hic() (in module instagraal.init_nuisance)
estimate_param_rippe() (in module instagraal.optim_rippe_curve_update)
estimate_parameters() (instagraal.cuda_lib_gl_single.sampler method)
estimate_parameters_rippe() (instagraal.cuda_lib_gl_single.sampler method)
eval_all_sub_likelihood() (instagraal.cuda_lib_gl_single.sampler method)
eval_likelihood() (instagraal.cuda_lib_gl_single.sampler method)
eval_likelihood_4_nuisance() (instagraal.cuda_lib_gl_single.sampler method)
eval_likelihood_init() (instagraal.cuda_lib_gl_single.sampler method)
eval_likelihood_on_mut() (instagraal.cuda_lib_gl_single.sampler method)
explode_genome() (instagraal.cuda_lib_gl_single.sampler method)
export_new_fasta() (instagraal.simu_single.simulation method)
external2internal() (in module instagraal.leastsqbound)
extract_current_sub_likelihood() (instagraal.cuda_lib_gl_single.sampler method)
extract_uniq_mutations() (instagraal.cuda_lib_gl_single.sampler method)
F
f_hic() (instagraal.cuda_lib_gl_single.sampler method)
f_rippe() (instagraal.cuda_lib_gl_single.sampler method)
file_len() (in module instagraal.pyramid_sparse)
fill_dist_all_mut() (instagraal.cuda_lib_gl_single.sampler method)
fill_dist_single() (instagraal.cuda_lib_gl_single.sampler method)
fill_dist_single_mut() (instagraal.cuda_lib_gl_single.sampler method)
fill_sparse_pyramid_level() (in module instagraal.pyramid_sparse)
fragment (class in instagraal.fragment)
free_gpu() (instagraal.cuda_lib_gl_single.sampler method)
full_em() (instagraal.instagraal.window method)
full_zoom_in_frag() (instagraal.pyramid_sparse.pyramid method)
G
generate_new_fasta() (instagraal.pyramid_sparse.level method)
genome_content() (instagraal.cuda_lib_gl_single.sampler method)
get_contig_info_from_file() (in module instagraal.pyramid_sparse)
get_frag_info_from_fil() (in module instagraal.pyramid_sparse)
get_level() (instagraal.pyramid_sparse.pyramid method)
get_packed() (instagraal.gpustruct.GPUStruct method)
get_ptr() (instagraal.gpustruct.GPUStruct method)
glinit() (instagraal.instagraal.window method)
glut_print() (instagraal.instagraal.window method)
GPUStruct (class in instagraal.gpustruct)
I
i2e_cov_x() (in module instagraal.leastsqbound)
init() (in module instagraal.glutil)
init_data() (instagraal.pyramid_sparse.level method)
init_frag_list() (in module instagraal.pyramid_sparse)
init_gl_image() (instagraal.simu_single.simulation method)
initiate() (instagraal.fragment.basic_fragment class method)
(instagraal.fragment.fragment class method)
insert_blocks() (instagraal.cuda_lib_gl_single.sampler method)
insert_repeats() (instagraal.cuda_lib_gl_single.sampler method)
instagraal (module)
instagraal.cuda_lib_gl_single (module)
instagraal.fragment (module)
instagraal.glutil (module)
instagraal.gpustruct (module)
instagraal.init_nuisance (module)
instagraal.instagraal (module)
instagraal.leastsqbound (module)
instagraal.log (module)
instagraal.optim_rippe_curve_update (module)
instagraal.pyramid_sparse (module)
instagraal.simu_single (module)
instagraal.vector (module)
instagraal.version (module)
internal2external() (in module instagraal.leastsqbound)
internal2external_grad() (in module instagraal.leastsqbound)
K
kth_diag_indices() (in module instagraal.simu_single)
L
leastsqbound() (in module instagraal.leastsqbound)
level (class in instagraal.pyramid_sparse)
lights() (in module instagraal.glutil)
load_data() (instagraal.pyramid_sparse.level method)
load_gl_buffers() (instagraal.simu_single.simulation method)
load_gl_cuda_tex_buffer() (instagraal.cuda_lib_gl_single.sampler method)
load_gl_cuda_vbo() (instagraal.cuda_lib_gl_single.sampler method)
load_reference_sequence() (instagraal.pyramid_sparse.pyramid method)
loadProgram() (instagraal.cuda_lib_gl_single.sampler method)
local_flip() (instagraal.cuda_lib_gl_single.sampler method)
log_peval() (in module instagraal.optim_rippe_curve_update)
log_residuals() (in module instagraal.init_nuisance)
(in module instagraal.optim_rippe_curve_update)
log_residuals_4_min() (in module instagraal.init_nuisance)
M
main() (in module instagraal.instagraal)
(in module instagraal.pyramid_sparse)
modify_genome() (instagraal.cuda_lib_gl_single.sampler method)
modify_gl_cuda_buffer() (instagraal.cuda_lib_gl_single.sampler method)
modify_image_thresh() (instagraal.cuda_lib_gl_single.sampler method)
(instagraal.instagraal.window method)
modify_param_simu() (instagraal.cuda_lib_gl_single.sampler method)
modify_sub_vect_frags() (instagraal.simu_single.simulation method)
modify_vect_frags() (instagraal.simu_single.simulation method)
N
new_remove_problematic_fragments() (in module instagraal.pyramid_sparse)
normalize() (in module instagraal.vector)
O
on_click() (instagraal.instagraal.window method)
on_key() (instagraal.instagraal.window method)
on_mouse_motion() (instagraal.instagraal.window method)
P
perform_mutations() (instagraal.cuda_lib_gl_single.sampler method)
peval() (in module instagraal.init_nuisance)
(in module instagraal.optim_rippe_curve_update)
plot_info_simu() (instagraal.simu_single.simulation method)
pop_out_pop_in() (instagraal.cuda_lib_gl_single.sampler method)
prepare_sparse_call() (instagraal.cuda_lib_gl_single.sampler method)
props (instagraal.vector.Vec attribute)
pyramid (class in instagraal.pyramid_sparse)
R
release() (instagraal.simu_single.simulation method)
remote_update() (instagraal.instagraal.window method)
remove_problematic_fragments() (in module instagraal.pyramid_sparse)
render() (instagraal.instagraal.window method)
render_image() (instagraal.instagraal.window method)
replay_simu() (instagraal.instagraal.window method)
residual_4_max_dist() (in module instagraal.init_nuisance)
(in module instagraal.optim_rippe_curve_update)
residuals() (in module instagraal.init_nuisance)
(in module instagraal.optim_rippe_curve_update)
return_neighbours() (instagraal.cuda_lib_gl_single.sampler method)
return_rippe_vals() (instagraal.cuda_lib_gl_single.sampler method)
S
sampler (class in instagraal.cuda_lib_gl_single)
save_behaviour_to_txt() (instagraal.instagraal.window method)
select_data_set() (instagraal.simu_single.simulation method)
select_repeated_frags() (instagraal.simu_single.simulation method)
set_jumping_distributions_parameters() (instagraal.cuda_lib_gl_single.sampler method)
setup_all_gpu_struct() (instagraal.cuda_lib_gl_single.sampler method)
setup_distri_frags() (instagraal.cuda_lib_gl_single.sampler method)
setup_model_parameters() (instagraal.cuda_lib_gl_single.sampler method)
setup_rippe_parameters() (instagraal.cuda_lib_gl_single.sampler method)
setup_rippe_parameters_4_simu() (instagraal.cuda_lib_gl_single.sampler method)
setup_simu() (instagraal.instagraal.window method)
setup_thrust_modules() (instagraal.cuda_lib_gl_single.sampler method)
show_sub_slice() (instagraal.cuda_lib_gl_single.sampler method)
simple_start() (instagraal.instagraal.window method)
simulation (class in instagraal.simu_single)
slice_sparse_mat() (instagraal.cuda_lib_gl_single.sampler method)
sparse_data_2_gpu() (instagraal.cuda_lib_gl_single.sampler method)
sparse_data_4_gl() (instagraal.cuda_lib_gl_single.sampler method)
start_EM() (instagraal.instagraal.window method)
start_EM_all() (instagraal.instagraal.window method)
start_EM_no_scrambled() (instagraal.instagraal.window method)
start_EM_nuisance() (instagraal.instagraal.window method)
start_MCMC() (instagraal.instagraal.window method)
start_MTM() (instagraal.instagraal.window method)
step_nuisance_parameters() (instagraal.cuda_lib_gl_single.sampler method)
step_sampler() (instagraal.cuda_lib_gl_single.sampler method)
step_sampler_debug() (instagraal.cuda_lib_gl_single.sampler method)
subsample_data_set() (in module instagraal.pyramid_sparse)
T
temperature() (instagraal.cuda_lib_gl_single.sampler method)
test_copy_struct() (instagraal.cuda_lib_gl_single.sampler method)
test_model() (instagraal.instagraal.window method)
test_thrust() (instagraal.cuda_lib_gl_single.sampler method)
timer() (instagraal.instagraal.window method)
transloc() (instagraal.cuda_lib_gl_single.sampler method)
U
update_name() (instagraal.fragment.fragment method)
update_neighbourhood() (instagraal.cuda_lib_gl_single.sampler method)
update_super_index() (instagraal.pyramid_sparse.pyramid method)
update_super_index_in_dict_contig() (instagraal.pyramid_sparse.pyramid method)
V
Vec (class in instagraal.vector)
W
window (class in instagraal.instagraal)
Z
zoom_in_area() (instagraal.pyramid_sparse.pyramid method)
zoom_in_frag() (instagraal.pyramid_sparse.pyramid method)
zoom_in_pixel() (instagraal.pyramid_sparse.pyramid method)
zoom_out_frag() (instagraal.pyramid_sparse.pyramid method)
zoom_out_pixel() (instagraal.pyramid_sparse.pyramid method)
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