Index

A

add_parent() (arg_needle_lib.ARGNode method) add_sample() (arg_needle_lib.ARG method) ARG (class in arg_needle_lib) arg_needle_lib module

arg_to_newick() (in module arg_needle_lib) arg_to_tskit() (in module arg_needle_lib) ARGEdge (class in arg_needle_lib) ARGNode (class in arg_needle_lib) association_diploid_all() (in module arg_needle_lib) association_diploid_mutation() (in module arg_needle_lib)

B

bitset_volume_map() (in module arg_needle_lib)

C

check_basic() (arg_needle_lib.ARG method) check_children() (arg_needle_lib.ARG method) check_roots() (arg_needle_lib.ARG method)

child (arg_needle_lib.ARGEdge property) chromosome (arg_needle_lib.ARG property) compute_grm() (in module arg_needle_lib)

D

DescendantList (class in arg_needle_lib)

deserialize_arg() (in module arg_needle_lib)

E

edge (arg_needle_lib.Mutation property) end (arg_needle_lib.ARG property) (arg_needle_lib.ARGEdge property) (arg_needle_lib.ARGNode property) (arg_needle_lib.Root property)

exact_arg_grm() (in module arg_needle_lib)

G

generate_m_mutations() (in module arg_needle_lib) generate_mutations() (in module arg_needle_lib) get_genotype() (in module arg_needle_lib) get_id_of_closest_site() (arg_needle_lib.ARG method) get_idx_of_first_mutation_left_of() (arg_needle_lib.ARG method) get_idx_of_first_mutation_right_of() (arg_needle_lib.ARG method) get_idx_of_mutation_closest_to() (arg_needle_lib.ARG method)

get_mutation_sites() (arg_needle_lib.ARG method) get_mutations() (arg_needle_lib.Site method) get_mutations_matrix() (in module arg_needle_lib) get_position() (arg_needle_lib.Site method) get_site() (arg_needle_lib.ARG method) get_sites() (arg_needle_lib.ARG method) gower_center() (in module arg_needle_lib)

H

haploid_grm_to_diploid() (in module arg_needle_lib)

height (arg_needle_lib.ARGNode property) (arg_needle_lib.Mutation property)

I

ID (arg_needle_lib.ARGNode property)

impute() (in module arg_needle_lib) is_leaf() (arg_needle_lib.ARG method)

K

kc2_length_stab() (in module arg_needle_lib)

kc2_special_stab() (in module arg_needle_lib) kc2_tmrca_sv_stab() (in module arg_needle_lib)

L

leaf_ids (arg_needle_lib.ARG property) local_volume() (in module arg_needle_lib)

lowest_mutated_edge() (arg_needle_lib.ARG method) lowest_mutated_edge_by_site() (arg_needle_lib.ARG method)

M

module arg_needle_lib monte_carlo_arg_grm() (in module arg_needle_lib) mrca() (arg_needle_lib.ARG method) Mutation (class in arg_needle_lib)

mutation_best() (in module arg_needle_lib) mutation_match() (in module arg_needle_lib) mutation_match_all() (in module arg_needle_lib) mutations() (arg_needle_lib.ARG method) (arg_needle_lib.ARGEdge method)

N

node (arg_needle_lib.Root property) node() (arg_needle_lib.ARG method) node_ids() (arg_needle_lib.ARG method) num_edges() (arg_needle_lib.ARG method)

num_lineages() (in module arg_needle_lib) num_mutations() (arg_needle_lib.ARG method) num_nodes() (arg_needle_lib.ARG method) num_samples() (arg_needle_lib.ARG method) num_sites() (arg_needle_lib.ARG method)

O

offset (arg_needle_lib.ARG property)

P

parent (arg_needle_lib.ARGEdge property) parent_edge_at() (arg_needle_lib.ARGNode method) parent_edges() (arg_needle_lib.ARGNode method) parent_starts() (arg_needle_lib.ARGNode method)

populate_children_and_roots() (arg_needle_lib.ARG method) populate_mutations_on_edges() (arg_needle_lib.ARG method) position (arg_needle_lib.Mutation property) print_threshold() (arg_needle_lib.DescendantList static method)

R

remove_parent() (arg_needle_lib.ARGNode method) reserved_samples (arg_needle_lib.ARG property) rf_resolve_stab() (in module arg_needle_lib) rf_total_variation_stab() (in module arg_needle_lib)

Root (class in arg_needle_lib) root_at() (arg_needle_lib.ARG method) root_starts() (arg_needle_lib.ARG method) row_column_center() (in module arg_needle_lib)

S

sample_names (arg_needle_lib.ARG property) serialize_arg() (in module arg_needle_lib) set_chromosome() (arg_needle_lib.ARG method) set_offset() (arg_needle_lib.ARG method) set_sites() (arg_needle_lib.ARG method) set_threshold() (arg_needle_lib.DescendantList static method)

Site (class in arg_needle_lib) site_id (arg_needle_lib.Mutation property) stab_return_all_bitsets() (in module arg_needle_lib) start (arg_needle_lib.ARG property) (arg_needle_lib.ARGEdge property) (arg_needle_lib.ARGNode property) (arg_needle_lib.Root property)

T

thread_sample() (arg_needle_lib.ARG method) threaded_samples (arg_needle_lib.ARG property)

total_volume() (in module arg_needle_lib) trim_arg() (in module arg_needle_lib) tskit_to_arg() (in module arg_needle_lib)

U

update_parent_end() (arg_needle_lib.ARGNode method)

update_parent_start() (arg_needle_lib.ARGNode method)

V

validate_serialized_arg() (in module arg_needle_lib)

W

write_bitsets() (in module arg_needle_lib)

write_grm() (in module arg_needle_lib) write_mutations_to_haps() (in module arg_needle_lib)