Index

B

b_c_d_given_a_to_dict_a_b_c_d() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) b_c_given_a_to_dict_a_b_c() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) b_given_a_to_dict_a_b() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat)

backtrack_viterbi() (in module itrails.int_optimizer) (in module itrails.optimizer) backward() (in module itrails.int_optimizer) (in module itrails.optimizer) bell_numbers() (in module itrails.trans_mat)

C

calc_emissions_double_JC69() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) calc_emissions_single_JC69() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) combine_by_omega() (in module itrails.helper_omegas) combine_states() (in module itrails.combine_states) (in module itrails.int_combine_states) combine_states_wrapper() (in module itrails.combine_states)

compute_matrices_end_wrapper() (in module itrails.run_markov_chain_AB) compute_matrices_start_end_wrapper() (in module itrails.run_markov_chain_AB) (in module itrails.run_markov_chain_ABC) compute_matrix_end() (in module itrails.run_markov_chain_AB) compute_matrix_start_end() (in module itrails.run_markov_chain_AB) (in module itrails.run_markov_chain_ABC) cutpoints_AB() (in module itrails.cutpoints) cutpoints_ABC() (in module itrails.cutpoints)

D

deep_identify() (in module itrails.deepest_ti) deep_identify_wrapper() (in module itrails.deepest_ti) deepest_parallel_inner() (in module itrails.run_markov_chain_ABC)

deepest_ti() (in module itrails.deepest_ti) deepest_worker_inner() (in module itrails.run_markov_chain_ABC) divide_starting_probs() (in module itrails.int_get_joint_prob_mat)

E

expm() (in module itrails.expm)

F

find_norevcoal() (in module itrails.trans_mat) find_revcoal_recomb() (in module itrails.trans_mat) flow_seq_representer() (in module itrails.yaml_helpers) FlowSeq (class in itrails.yaml_helpers) forward() (in module itrails.int_optimizer) (in module itrails.optimizer)

forward_loglik() (in module itrails.int_optimizer) (in module itrails.optimizer) forward_loglik_par() (in module itrails.int_optimizer) (in module itrails.optimizer)

G

get_AB_precomp() (in module itrails.get_tab) get_ABC_precomp() (in module itrails.get_tab) get_emission_prob_mat() (in module itrails.get_emission_prob_mat) get_emission_prob_mat_introgression() (in module itrails.int_get_emission_prob_mat) get_idx_state() (in module itrails.read_data) get_idx_state_new_method() (in module itrails.read_data) get_joint_prob_mat() (in module itrails.get_joint_prob_mat) get_joint_prob_mat_introgression() (in module itrails.int_get_joint_prob_mat) get_obs_state_dct() (in module itrails.read_data)

get_obs_state_dct_new_method() (in module itrails.read_data) get_omega_nonrev_counts() (in module itrails.trans_mat) get_ordered() (in module itrails.int_get_ordered) get_tab_AB() (in module itrails.get_tab) get_tab_AB_introgression() (in module itrails.int_get_tab) get_tab_ABC() (in module itrails.get_tab) get_tab_ABC_introgression() (in module itrails.int_get_tab) get_times() (in module itrails.cutpoints) (in module itrails.int_get_times) get_trans_mat() (in module itrails.trans_mat)

I

init_worker() (in module itrails.int_shared_data) instant_mat() (in module itrails.int_vanloan) itrails.combine_states module itrails.cutpoints module itrails.deepest_ti module itrails.expm module itrails.get_emission_prob_mat module itrails.get_joint_prob_mat module itrails.get_tab module itrails.get_trans_emiss module itrails.helper_omegas module itrails.int_combine_states module itrails.int_get_emission_prob_mat module itrails.int_get_joint_prob_mat module itrails.int_get_ordered module itrails.int_get_tab module itrails.int_get_times module itrails.int_get_trans_emiss module itrails.int_load_trans_mat module

itrails.int_optimizer module itrails.int_shared_data module itrails.int_vanloan module itrails.ncpu module itrails.optimizer module itrails.read_data module itrails.run_markov_chain_AB module itrails.run_markov_chain_ABC module itrails.trans_mat module itrails.vanloan module itrails.workflow_int_optimize module itrails.workflow_int_posterior module itrails.workflow_int_viterbi module itrails.workflow_optimize module itrails.workflow_posterior module itrails.workflow_viterbi module itrails.yaml_helpers module

J

JC69_analytical_integral() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat)

JC69_analytical_integral_double() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat)

L

load_config() (in module itrails.yaml_helpers) load_trans_mat() (in module itrails.int_load_trans_mat) load_trans_mat_miss() (in module itrails.int_get_joint_prob_mat) loglik_wrapper() (in module itrails.int_optimizer) (in module itrails.optimizer)

loglik_wrapper_new_method() (in module itrails.int_optimizer) (in module itrails.optimizer) loglik_wrapper_par() (in module itrails.int_optimizer) (in module itrails.optimizer) loglik_wrapper_par_new_method() (in module itrails.int_optimizer) (in module itrails.optimizer)

M

maf_parser() (in module itrails.read_data) maf_parser_new_method() (in module itrails.read_data) main() (in module itrails.workflow_int_optimize) (in module itrails.workflow_int_posterior) (in module itrails.workflow_int_viterbi) (in module itrails.workflow_optimize) (in module itrails.workflow_posterior) (in module itrails.workflow_viterbi) mix_probs() (in module itrails.int_get_tab) module itrails.combine_states itrails.cutpoints itrails.deepest_ti itrails.expm itrails.get_emission_prob_mat itrails.get_joint_prob_mat itrails.get_tab itrails.get_trans_emiss itrails.helper_omegas itrails.int_combine_states itrails.int_get_emission_prob_mat itrails.int_get_joint_prob_mat itrails.int_get_ordered itrails.int_get_tab itrails.int_get_times itrails.int_get_trans_emiss itrails.int_load_trans_mat itrails.int_optimizer itrails.int_shared_data itrails.int_vanloan itrails.ncpu itrails.optimizer itrails.read_data itrails.run_markov_chain_AB itrails.run_markov_chain_ABC itrails.trans_mat itrails.vanloan itrails.workflow_int_optimize itrails.workflow_int_posterior itrails.workflow_int_viterbi itrails.workflow_optimize itrails.workflow_posterior itrails.workflow_viterbi itrails.yaml_helpers

N

number_array_1() (in module itrails.trans_mat)

number_array_2() (in module itrails.trans_mat) number_array_3() (in module itrails.trans_mat)

O

optimization_wrapper() (in module itrails.optimizer) optimization_wrapper_introgression() (in module itrails.int_optimizer)

optimizer() (in module itrails.optimizer) optimizer_introgression() (in module itrails.int_optimizer)

P

p_b_c_d_given_a_JC69_analytical() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) p_b_c_given_a_JC69_analytical() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) p_b_given_a() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat) parse_coordinates() (in module itrails.read_data) partition() (in module itrails.trans_mat)

pool_AB() (in module itrails.get_tab) pool_AB_total() (in module itrails.int_get_tab) pool_ABC() (in module itrails.get_tab) post_prob() (in module itrails.int_optimizer) (in module itrails.optimizer) post_prob_wrapper() (in module itrails.int_optimizer) (in module itrails.optimizer) precomp() (in module itrails.get_tab)

R

rate_mat_JC69() (in module itrails.get_emission_prob_mat) (in module itrails.int_get_emission_prob_mat)

remove_absorbing_indices() (in module itrails.helper_omegas) run_markov_chain_AB() (in module itrails.run_markov_chain_AB) run_markov_chain_ABC() (in module itrails.run_markov_chain_ABC)

S

set_partitions() (in module itrails.trans_mat)

split_migration() (in module itrails.int_get_joint_prob_mat)

T

trans_emiss_calc() (in module itrails.get_trans_emiss) trans_emiss_calc_introgression() (in module itrails.int_get_trans_emiss)

trans_mat_num() (in module itrails.int_load_trans_mat) translate_to_minimum() (in module itrails.trans_mat) translate_to_omega() (in module itrails.helper_omegas)

U

update_best_model() (in module itrails.yaml_helpers)

update_n_cpu() (in module itrails.ncpu)

V

vanloan() (in module itrails.vanloan) vanloan_1() (in module itrails.int_vanloan) vanloan_2() (in module itrails.int_vanloan) vanloan_3() (in module itrails.int_vanloan) vanloan_identify() (in module itrails.vanloan) vanloan_identify_wrapper() (in module itrails.vanloan) vanloan_parallel_inner() (in module itrails.run_markov_chain_ABC)

vanloan_worker_inner() (in module itrails.run_markov_chain_ABC) viterbi() (in module itrails.int_optimizer) (in module itrails.optimizer) viterbi_old() (in module itrails.int_optimizer) (in module itrails.optimizer) viterbi_wrapper() (in module itrails.int_optimizer) (in module itrails.optimizer)

W

wrapper_state_1() (in module itrails.trans_mat) wrapper_state_2() (in module itrails.trans_mat) wrapper_state_3() (in module itrails.trans_mat) wrapper_state_general() (in module itrails.trans_mat)

write_info_AB() (in module itrails.int_shared_data) write_info_ABC() (in module itrails.int_shared_data) write_list() (in module itrails.int_optimizer) (in module itrails.optimizer)