Documentation Report

Classes and methods that start with a single underscore are excluded from the report

Red rows have a docstring, but are not in Sphinx, yellow have neither

Module: text_formats

Isolated Functions

Name	Type	Has Docstring	In Sphinx
parse_fam	function	✓	✗
flexible_file_output	function	✓	✗
write_nexus	function	✗	✗
wrap_text	function	✓	✗
write_fasta	function	✗	✗
build_newick	function	✓	✗
dump_text	function	✗	✗
text_metadata	function	✗	✗
f	function	✗	✗

Module: combinatorics

Isolated Functions

Name	Type	Has Docstring	In Sphinx
equal_chunks	function	✓	✗
generate_star	function	✓	✗
generate_comb	function	✓	✗
generate_balanced	function	✓	✗
generate_random_binary	function	✓	✗
split_polytomies	function	✓	✗
treeseq_count_topologies	function	✗	✗
tree_count_topologies	function	✗	✗
combine_child_topologies	function	✓	✗
all_trees	function	✓	✓
all_tree_shapes	function	✓	✓
all_tree_labellings	function	✓	✓
num_shapes	function	✓	✗
num_tree_pairings	function	✓	✗
num_labellings	function	✗	✗
children_shape_ranks	function	✓	✗
children_label_ranks	function	✓	✗
group_rank	function	✗	✗
num_list_of_group_labellings	function	✓	✗
num_group_labellings	function	✓	✗
num_assignments_in_group	function	✓	✗
group_label_ranks	function	✓	✗
set_minus	function	✗	✗
partitions	function	✓	✗
rule_asc	function	✓	✗
group_by	function	✗	✗
group_partition	function	✗	✗
merge_tuple	function	✗	✗
isdisjoint	function	✗	✗
update_state	function	✗	✗
assign_internal_labels	function	✗	✗
reorder_children	function	✗	✗
add_node	function	✗	✗
same_num_leaves	function	✗	✗
same_shape	function	✗	✗

Class: Rank

Name	Type	Has Docstring	In Sphinx
Rank	class	✓	✓

Class: TreeNode

Name	Type	Has Docstring	In Sphinx
TreeNode	class	✓	✗
as_tables	function	✓	✗
random_binary_tree	function	✓	✗
balanced_tree	function	✓	✗

Class: TopologyCounter

Name	Type	Has Docstring	In Sphinx
TopologyCounter	class	✓	✓
merge	function	✓	✗
from_sample	function	✓	✗

Class: PartialTopologyCounter

Name	Type	Has Docstring	In Sphinx
PartialTopologyCounter	class	✓	✗
add_sibling_topologies	function	✓	✗
join_all_combinations	function	✓	✗
join_topologies	function	✗	✗

Class: RankTree

Name	Type	Has Docstring	In Sphinx
RankTree	class	✓	✗
compute_shape_rank	function	✓	✗
compute_label_rank	function	✓	✗
num_labellings	function	✗	✗
rank	function	✗	✗
shape_rank	function	✗	✗
label_rank	function	✗	✗
unrank	function	✓	✗
shape_unrank	function	✓	✗
label_unrank	function	✓	✗
canonical_order	function	✓	✗
from_tsk_tree_node	function	✗	✗
from_tsk_tree	function	✗	✗
to_tsk_tree	function	✓	✗
all_labelled_trees	function	✓	✗
all_unlabelled_trees	function	✓	✗
all_subtree_pairings	function	✗	✗
all_labellings	function	✓	✗
label_all_groups	function	✗	✗
label_tree_group	function	✗	✗
newick	function	✗	✗
label	function	✗	✗
labelled	function	✗	✗
min_label	function	✗	✗
is_leaf	function	✗	✗
leaf_partition	function	✗	✗
group_children_by_num_leaves	function	✗	✗
group_children_by_shape	function	✗	✗
shape_equal	function	✗	✗
is_canonical	function	✗	✗
is_symmetrical	function	✗	✗

Class: Combination

Name	Type	Has Docstring	In Sphinx
Combination	class	✗	✗
comb	function	✓	✗
comb_with_replacement	function	✓	✗
rank	function	✓	✗
from_range_rank	function	✓	✗
unrank	function	✗	✗
with_replacement_rank	function	✓	✗
with_replacement_unrank	function	✓	✗

Module: genotypes

Isolated Functions

Name	Type	Has Docstring	In Sphinx
allele_remap	function	✗	✗

Class: Variant

Name	Type	Has Docstring	In Sphinx
Variant	class	✓	✓
site	function	✓	✓
alleles	function	✓	✓
samples	function	✓	✓
genotypes	function	✓	✓
isolated_as_missing	function	✓	✓
has_missing_data	function	✓	✓
num_missing	function	✓	✓
num_alleles	function	✓	✓
position	function	✗	✗
index	function	✗	✗
decode	function	✓	✓
copy	function	✓	✓
states	function	✓	✓
counts	function	✓	✓
frequencies	function	✓	✓

Module: intervals

Isolated Functions

Name	Type	Has Docstring	In Sphinx

Class: RateMap

Name	Type	Has Docstring	In Sphinx
RateMap	class	✓	✗
left	function	✓	✗
right	function	✓	✗
mid	function	✓	✗
span	function	✓	✗
position	function	✓	✗
rate	function	✓	✗
mass	function	✓	✗
missing	function	✓	✗
non_missing	function	✓	✗
num_intervals	function	✓	✗
num_missing_intervals	function	✓	✗
num_non_missing_intervals	function	✓	✗
sequence_length	function	✓	✗
total_mass	function	✓	✗
mean_rate	function	✓	✗
get_rate	function	✓	✗
get_cumulative_mass	function	✓	✗
find_index	function	✓	✗
missing_intervals	function	✓	✗
asdict	function	✗	✗
copy	function	✓	✗
slice	function	✓	✗
uniform	function	✓	✗
read_hapmap	function	✓	✗

Module: util

Isolated Functions

Name	Type	Has Docstring	In Sphinx
canonical_json	function	✓	✗
is_unknown_time	function	✓	✓
safe_np_int_cast	function	✓	✗
pack_bytes	function	✓	✓
unpack_bytes	function	✓	✓
pack_strings	function	✓	✓
unpack_strings	function	✓	✓
pack_arrays	function	✓	✗
unpack_arrays	function	✓	✗
intervals_to_np_array	function	✓	✗
negate_intervals	function	✓	✗
naturalsize	function	✓	✗
obj_to_collapsed_html	function	✓	✗
truncate_string_end	function	✓	✗
render_metadata	function	✗	✗
unicode_table	function	✓	✗
html_table	function	✗	✗
tree_sequence_html	function	✗	✗
tree_html	function	✗	✗
variant_html	function	✗	✗
convert_file_like_to_open_file	function	✗	✗
set_print_options	function	✓	✗
truncate_rows	function	✓	✗
random_nucleotides	function	✓	✓
raise_known_file_format_errors	function	✓	✗

Class: Dataclass

Name	Type	Has Docstring	In Sphinx
Dataclass	class	✗	✗
replace	function	✓	✗
asdict	function	✓	✗

Module: formats

Isolated Functions

Name	Type	Has Docstring	In Sphinx
get_h5py	function	✗	✗
load_legacy	function	✓	✗
dump_legacy	function	✓	✗

Module: stats

Isolated Functions

Name	Type	Has Docstring	In Sphinx

Class: LdCalculator

Name	Type	Has Docstring	In Sphinx
LdCalculator	class	✓	✓
get_r2	function	✗	✗
r2	function	✓	✓
get_r2_array	function	✗	✗
r2_array	function	✓	✓
get_r2_matrix	function	✗	✗
r2_matrix	function	✓	✓

Module: trees

Isolated Functions

Name	Type	Has Docstring	In Sphinx
store_tree_sequence	function	✗	✗
load	function	✓	✓
parse_individuals	function	✓	✓
parse_nodes	function	✓	✓
parse_edges	function	✓	✓
parse_sites	function	✓	✓
parse_mutations	function	✓	✓
parse_populations	function	✓	✓
parse_migrations	function	✓	✓
load_text	function	✓	✓
write_ms	function	✓	✗
new_init	function	✗	✗
traverse	function	✗	✗
worker	function	✗	✗
tjd_func	function	✗	✗
fst_func	function	✗	✗

Class: CoalescenceRecord

Name	Type	Has Docstring	In Sphinx
CoalescenceRecord	class	✗	✗

Class: Interval

Name	Type	Has Docstring	In Sphinx
Interval	class	✓	✓
span	function	✓	✓
mid	function	✓	✓

Class: EdgeDiff

Name	Type	Has Docstring	In Sphinx
EdgeDiff	class	✗	✗

Class: Individual

Name	Type	Has Docstring	In Sphinx
Individual	class	✓	✓
population	function	✗	✗
time	function	✗	✗

Class: Node

Name	Type	Has Docstring	In Sphinx
Node	class	✓	✓
is_sample	function	✓	✓

Class: Edge

Name	Type	Has Docstring	In Sphinx
Edge	class	✓	✓
span	function	✓	✓
interval	function	✓	✓

Class: Site

Name	Type	Has Docstring	In Sphinx
Site	class	✓	✓
alleles	function	✓	✓

Class: Mutation

Name	Type	Has Docstring	In Sphinx
Mutation	class	✓	✓

Class: Migration

Name	Type	Has Docstring	In Sphinx
Migration	class	✓	✓

Class: Population

Name	Type	Has Docstring	In Sphinx
Population	class	✓	✓

Class: Edgeset

Name	Type	Has Docstring	In Sphinx
Edgeset	class	✗	✗

Class: Provenance

Name	Type	Has Docstring	In Sphinx
Provenance	class	✓	✓

Class: Tree

Name	Type	Has Docstring	In Sphinx
Tree	class	✓	✓
copy	function	✓	✓
tree_sequence	function	✓	✓
root_threshold	function	✓	✓
first	function	✓	✓
last	function	✓	✓
next	function	✓	✓
prev	function	✓	✓
clear	function	✓	✓
seek_index	function	✓	✓
seek	function	✓	✓
rank	function	✓	✓
unrank	function	✓	✓
count_topologies	function	✓	✓
get_branch_length	function	✗	✗
branch_length	function	✓	✓
get_total_branch_length	function	✗	✗
total_branch_length	function	✓	✓
get_mrca	function	✗	✗
mrca	function	✓	✓
get_tmrca	function	✗	✗
tmrca	function	✓	✓
get_parent	function	✗	✗
parent	function	✓	✓
parent_array	function	✓	✓
ancestors	function	✓	✓
left_child	function	✓	✓
left_child_array	function	✓	✓
right_child	function	✓	✓
right_child_array	function	✓	✓
left_sib	function	✓	✓
left_sib_array	function	✓	✓
right_sib	function	✓	✓
right_sib_array	function	✓	✓
siblings	function	✓	✓
num_children_array	function	✓	✓
edge	function	✓	✓
edge_array	function	✓	✓
left_sample	function	✗	✗
right_sample	function	✗	✗
next_sample	function	✗	✗
virtual_root	function	✓	✓
num_edges	function	✓	✓
left_root	function	✓	✓
right_root	function	✗	✗
get_children	function	✗	✗
children	function	✓	✓
get_time	function	✗	✗
time	function	✓	✓
depth	function	✓	✓
get_population	function	✗	✗
population	function	✓	✓
is_internal	function	✓	✓
is_leaf	function	✓	✓
is_isolated	function	✓	✓
is_sample	function	✓	✓
is_descendant	function	✓	✓
num_nodes	function	✓	✓
num_roots	function	✓	✓
has_single_root	function	✓	✓
has_multiple_roots	function	✓	✓
roots	function	✓	✓
get_root	function	✗	✗
root	function	✓	✓
is_root	function	✓	✓
get_index	function	✗	✗
index	function	✓	✓
get_interval	function	✗	✗
interval	function	✓	✓
get_length	function	✗	✗
length	function	✗	✗
span	function	✓	✓
mid	function	✓	✓
get_sample_size	function	✗	✗
sample_size	function	✗	✗
draw_text	function	✓	✓
draw_svg	function	✓	✓
draw	function	✓	✓
get_num_mutations	function	✗	✗
num_mutations	function	✓	✓
num_sites	function	✓	✓
sites	function	✓	✓
mutations	function	✓	✓
get_leaves	function	✗	✗
leaves	function	✓	✓
samples	function	✓	✓
num_children	function	✓	✓
get_num_leaves	function	✗	✗
get_num_samples	function	✗	✗
num_samples	function	✓	✓
get_num_tracked_leaves	function	✗	✗
get_num_tracked_samples	function	✗	✗
num_tracked_samples	function	✓	✓
preorder	function	✓	✓
postorder	function	✓	✓
timeasc	function	✓	✓
timedesc	function	✓	✓
nodes	function	✓	✓
as_newick	function	✓	✓
newick	function	✓	✓
as_dict_of_dicts	function	✓	✓
parent_dict	function	✗	✗
get_parent_dict	function	✗	✗
map_mutations	function	✓	✓
kc_distance	function	✓	✓
rf_distance	function	✓	✓
path_length	function	✓	✓
distance_between	function	✓	✓
b1_index	function	✓	✓
b2_index	function	✓	✓
colless_index	function	✓	✓
sackin_index	function	✓	✓
num_lineages	function	✓	✓
split_polytomies	function	✓	✓
generate_star	function	✓	✓
generate_balanced	function	✓	✓
generate_comb	function	✓	✓
generate_random_binary	function	✓	✓

Class: TreeIterator

Name	Type	Has Docstring	In Sphinx
TreeIterator	class	✓	✗

Class: SimpleContainerSequence

Name	Type	Has Docstring	In Sphinx
SimpleContainerSequence	class	✓	✗

Class: TableMetadataSchemas

Name	Type	Has Docstring	In Sphinx
TableMetadataSchemas	class	✓	✓

Class: TreeSequence

Name	Type	Has Docstring	In Sphinx
TreeSequence	class	✓	✓
equals	function	✓	✓
ll_tree_sequence	function	✗	✗
get_ll_tree_sequence	function	✗	✗
aslist	function	✓	✓
load	function	✗	✗
load_tables	function	✗	✗
dump	function	✓	✓
reference_sequence	function	✓	✓
has_reference_sequence	function	✓	✓
tables_dict	function	✓	✓
tables	function	✓	✓
nbytes	function	✓	✓
dump_tables	function	✓	✓
dump_text	function	✓	✓
num_samples	function	✓	✓
table_metadata_schemas	function	✓	✓
sample_size	function	✗	✗
get_sample_size	function	✗	✗
file_uuid	function	✗	✗
discrete_genome	function	✓	✓
discrete_time	function	✓	✓
min_time	function	✓	✓
max_time	function	✓	✓
sequence_length	function	✓	✓
get_sequence_length	function	✗	✗
metadata	function	✓	✓
metadata_schema	function	✓	✓
time_units	function	✓	✓
num_edges	function	✓	✓
get_num_trees	function	✗	✗
num_trees	function	✓	✓
get_num_sites	function	✗	✗
num_sites	function	✓	✓
get_num_mutations	function	✗	✗
num_mutations	function	✓	✓
get_num_nodes	function	✗	✗
num_individuals	function	✓	✓
num_nodes	function	✓	✓
num_provenances	function	✓	✓
num_populations	function	✓	✓
num_migrations	function	✓	✓
max_root_time	function	✓	✓
migrations	function	✓	✓
individuals	function	✓	✓
nodes	function	✓	✓
edges	function	✓	✓
edgesets	function	✗	✗
edge_diffs	function	✓	✓
sites	function	✓	✓
mutations	function	✓	✓
populations	function	✓	✓
provenances	function	✓	✓
breakpoints	function	✓	✓
at	function	✓	✓
at_index	function	✓	✓
first	function	✓	✓
last	function	✓	✓
trees	function	✓	✓
coiterate	function	✓	✓
haplotypes	function	✓	✓
variants	function	✓	✓
genotype_matrix	function	✓	✓
alignments	function	✓	✓
individuals_population	function	✓	✓
individual_populations	function	✗	✗
individuals_time	function	✓	✓
individual_times	function	✗	✗
individuals_location	function	✓	✓
individual_locations	function	✗	✗
individuals_flags	function	✓	✓
nodes_time	function	✓	✓
nodes_flags	function	✓	✓
nodes_population	function	✓	✓
nodes_individual	function	✓	✓
edges_left	function	✓	✓
edges_right	function	✓	✓
edges_parent	function	✓	✓
edges_child	function	✓	✓
sites_position	function	✓	✓
mutations_site	function	✓	✓
mutations_node	function	✓	✓
mutations_parent	function	✓	✓
mutations_time	function	✓	✓
migrations_left	function	✓	✓
migrations_right	function	✓	✓
migrations_node	function	✓	✓
migrations_source	function	✓	✓
migrations_dest	function	✓	✓
migrations_time	function	✓	✓
indexes_edge_insertion_order	function	✓	✓
indexes_edge_removal_order	function	✓	✓
individual	function	✓	✓
node	function	✓	✓
check_index	function	✗	✗
edge	function	✓	✓
migration	function	✓	✓
mutation	function	✓	✓
site	function	✓	✓
population	function	✓	✓
provenance	function	✓	✓
get_samples	function	✗	✗
samples	function	✓	✓
as_vcf	function	✓	✓
write_vcf	function	✓	✓
write_fasta	function	✓	✓
as_fasta	function	✓	✓
write_nexus	function	✓	✓
as_nexus	function	✓	✓
to_macs	function	✓	✓
simplify	function	✓	✓
delete_sites	function	✓	✓
delete_intervals	function	✓	✓
keep_intervals	function	✓	✓
ltrim	function	✓	✓
rtrim	function	✓	✓
trim	function	✓	✓
split_edges	function	✓	✓
decapitate	function	✓	✓
extend_haplotypes	function	✓	✓
subset	function	✓	✓
union	function	✓	✓
draw_svg	function	✓	✓
draw_text	function	✓	✓
general_stat	function	✓	✓
sample_count_stat	function	✓	✓
parse_windows	function	✗	✗
parse_sites	function	✗	✗
parse_positions	function	✗	✗
diversity	function	✓	✓
divergence	function	✓	✓
divergence_matrix	function	✗	✗
genetic_relatedness	function	✓	✓
genetic_relatedness_matrix	function	✓	✓
genetic_relatedness_weighted	function	✓	✓
genetic_relatedness_vector	function	✓	✓
trait_covariance	function	✓	✓
trait_correlation	function	✓	✓
trait_regression	function	✓	✓
trait_linear_model	function	✓	✓
segregating_sites	function	✓	✓
allele_frequency_spectrum	function	✓	✓
Tajimas_D	function	✓	✓
Fst	function	✓	✓
Y3	function	✓	✓
Y2	function	✓	✓
Y1	function	✓	✓
f4	function	✓	✓
f3	function	✓	✓
f2	function	✓	✓
mean_descendants	function	✓	✓
genealogical_nearest_neighbours	function	✓	✓
kc_distance	function	✓	✓
count_topologies	function	✓	✓
ibd_segments	function	✓	✓
pair_coalescence_counts	function	✓	✓
pair_coalescence_quantiles	function	✓	✓
pair_coalescence_rates	function	✓	✓
impute_unknown_mutations_time	function	✓	✓
ld_matrix	function	✗	✗
get_pairwise_diversity	function	✗	✗
pairwise_diversity	function	✓	✓
get_time	function	✗	✗
get_population	function	✗	✗
records	function	✗	✗
get_num_records	function	✗	✗
diffs	function	✗	✗
newick_trees	function	✗	✗
to_nexus	function	✗	✗

Module: drawing

Isolated Functions

Name	Type	Has Docstring	In Sphinx
check_orientation	function	✗	✗
check_max_time	function	✗	✗
check_min_time	function	✗	✗
check_time_scale	function	✗	✗
check_format	function	✗	✗
check_order	function	✓	✗
check_x_scale	function	✓	✗
check_x_lim	function	✓	✗
create_tick_labels	function	✓	✗
clip_ts	function	✓	✗
check_y_ticks	function	✓	✗
rnd	function	✓	✗
bold_integer	function	✗	✗
edge_and_sample_nodes	function	✓	✗
draw_tree	function	✗	✗
add_class	function	✓	✗
to_np_unicode	function	✓	✗
get_left_neighbour	function	✓	✗
get_left_child	function	✓	✗
node_time_depth	function	✓	✗
find_neighbours	function	✗	✗
remap_style	function	✗	✗

Class: Offsets

Name	Type	Has Docstring	In Sphinx
Offsets	class	✓	✗

Class: Timescaling

Name	Type	Has Docstring	In Sphinx
Timescaling	class	✓	✗
log_transform	function	✓	✗
linear_transform	function	✗	✗

Class: SVGString

Name	Type	Has Docstring	In Sphinx
SVGString	class	✓	✓

Class: Plotbox

Name	Type	Has Docstring	In Sphinx
Plotbox	class	✗	✗
set_padding	function	✗	✗
max_x	function	✗	✗
max_y	function	✗	✗
top	function	✗	✗
left	function	✗	✗
bottom	function	✗	✗
right	function	✗	✗
width	function	✗	✗
height	function	✗	✗
draw	function	✗	✗

Class: SvgPlot

Name	Type	Has Docstring	In Sphinx
SvgPlot	class	✓	✗
get_plotbox	function	✓	✗
add_text_in_group	function	✓	✗

Class: SvgSkippedPlot

Name	Type	Has Docstring	In Sphinx
SvgSkippedPlot	class	✗	✗

Class: SvgAxisPlot

Name	Type	Has Docstring	In Sphinx
SvgAxisPlot	class	✓	✗
set_spacing	function	✓	✗
get_axes	function	✗	✗
draw_x_axis	function	✗	✗
draw_y_axis	function	✗	✗
shade_background	function	✗	✗
x_transform	function	✗	✗

Class: SvgTreeSequence

Name	Type	Has Docstring	In Sphinx
SvgTreeSequence	class	✓	✗
find_used_trees	function	✓	✗
draw_x_axis	function	✓	✗

Class: SvgTree

Name	Type	Has Docstring	In Sphinx
SvgTree	class	✓	✗
process_mutations_over_node	function	✓	✗
assign_y_coordinates	function	✓	✗
assign_x_coordinates	function	✗	✗
info_classes	function	✓	✗
text_transform	function	✗	✗
draw_tree	function	✗	✗

Class: TextTreeSequence

Name	Type	Has Docstring	In Sphinx
TextTreeSequence	class	✓	✗

Class: TextTree

Name	Type	Has Docstring	In Sphinx
TextTree	class	✓	✗

Class: VerticalTextTree

Name	Type	Has Docstring	In Sphinx
VerticalTextTree	class	✓	✗
default_node_label	function	✗	✗

Class: HorizontalTextTree

Name	Type	Has Docstring	In Sphinx
HorizontalTextTree	class	✓	✗
default_node_label	function	✗	✗

Module: provenance

Isolated Functions

Name	Type	Has Docstring	In Sphinx
get_environment	function	✓	✗
get_resources	function	✗	✗
get_provenance_dict	function	✓	✗
get_schema	function	✓	✗
validate_provenance	function	✓	✓

Module: cli

Isolated Functions

Name	Type	Has Docstring	In Sphinx
set_sigpipe_handler	function	✗	✗
sys_exit	function	✗	✗
load_tree_sequence	function	✗	✗
run_info	function	✗	✗
run_trees	function	✗	✗
run_upgrade	function	✗	✗
run_individuals	function	✗	✗
run_nodes	function	✗	✗
run_edges	function	✗	✗
run_sites	function	✗	✗
run_mutations	function	✗	✗
run_populations	function	✗	✗
run_migrations	function	✗	✗
run_provenances	function	✗	✗
run_fasta	function	✗	✗
run_vcf	function	✗	✗
add_tree_sequence_argument	function	✗	✗
add_precision_argument	function	✗	✗
get_tskit_parser	function	✗	✗
tskit_main	function	✗	✗

Module: metadata

Isolated Functions

Name	Type	Has Docstring	In Sphinx
replace_root_refs	function	✗	✗
register_metadata_codec	function	✓	✓
binary_format_validator	function	✗	✗
required_validator	function	✗	✗
validate_bytes	function	✗	✗
parse_metadata_schema	function	✓	✗
lazy_decode	function	✗	✗
array_decode	function	✗	✗
array_decode_exhaust	function	✗	✗
decode_object_or_null	function	✗	✗
object_encode	function	✗	✗
enforce_fixed_properties	function	✗	✗
decode_string	function	✗	✗
padding_decode	function	✗	✗
array_encode_with_length	function	✗	✗
new_init	function	✗	✗

Class: AbstractMetadataCodec

Name	Type	Has Docstring	In Sphinx
AbstractMetadataCodec	class	✓	✗
modify_schema	function	✗	✗
is_schema_trivial	function	✗	✗
encode	function	✗	✗
decode	function	✗	✗

Class: JSONCodec

Name	Type	Has Docstring	In Sphinx
JSONCodec	class	✗	✗
default_validator	function	✗	✗
is_schema_trivial	function	✗	✗
encode	function	✗	✗
decode	function	✗	✗

Class: NOOPCodec

Name	Type	Has Docstring	In Sphinx
NOOPCodec	class	✗	✗
encode	function	✗	✗
decode	function	✗	✗

Class: StructCodec

Name	Type	Has Docstring	In Sphinx
StructCodec	class	✓	✗
order_by_index	function	✓	✗
make_decode	function	✓	✗
make_array_decode	function	✗	✗
make_object_decode	function	✗	✗
make_object_or_null_decode	function	✗	✗
make_string_decode	function	✗	✗
make_null_decode	function	✗	✗
make_numeric_decode	function	✗	✗
make_encode	function	✓	✗
make_array_encode	function	✗	✗
make_object_encode	function	✗	✗
make_object_or_null_encode	function	✗	✗
make_string_encode	function	✗	✗
make_null_encode	function	✗	✗
make_numeric_encode	function	✗	✗
modify_schema	function	✗	✗
encode	function	✗	✗
decode	function	✗	✗

Class: MetadataSchema

Name	Type	Has Docstring	In Sphinx
MetadataSchema	class	✓	✓
schema	function	✗	✗
asdict	function	✓	✓
validate_and_encode_row	function	✓	✓
decode_row	function	✓	✓
encode_row	function	✓	✓
permissive_json	function	✓	✓
null	function	✓	✓

Class: _CachedMetadata

Name	Type	Has Docstring	In Sphinx

Class: MetadataProvider

Name	Type	Has Docstring	In Sphinx
MetadataProvider	class	✓	✗
metadata_schema	function	✗	✗
metadata	function	✗	✗
metadata_bytes	function	✓	✗
nbytes	function	✗	✗
assert_equals	function	✗	✗

Module: tables

Isolated Functions

Name	Type	Has Docstring	In Sphinx
keep_with_offset	function	✓	✗
getter	function	✗	✗

Class: NotSetMeta

Name	Type	Has Docstring	In Sphinx
NotSetMeta	class	✗	✗

Class: NOTSET

Name	Type	Has Docstring	In Sphinx
NOTSET	class	✗	✗

Class: IndividualTableRow

Name	Type	Has Docstring	In Sphinx
IndividualTableRow	class	✓	✓

Class: NodeTableRow

Name	Type	Has Docstring	In Sphinx
NodeTableRow	class	✓	✓

Class: EdgeTableRow

Name	Type	Has Docstring	In Sphinx
EdgeTableRow	class	✓	✓

Class: MigrationTableRow

Name	Type	Has Docstring	In Sphinx
MigrationTableRow	class	✓	✓

Class: SiteTableRow

Name	Type	Has Docstring	In Sphinx
SiteTableRow	class	✓	✓

Class: MutationTableRow

Name	Type	Has Docstring	In Sphinx
MutationTableRow	class	✓	✓

Class: PopulationTableRow

Name	Type	Has Docstring	In Sphinx
PopulationTableRow	class	✓	✓

Class: ProvenanceTableRow

Name	Type	Has Docstring	In Sphinx
ProvenanceTableRow	class	✓	✓

Class: TableCollectionIndexes

Name	Type	Has Docstring	In Sphinx
TableCollectionIndexes	class	✓	✓
asdict	function	✗	✓
nbytes	function	✓	✓

Class: BaseTable

Name	Type	Has Docstring	In Sphinx
BaseTable	class	✓	✗
num_rows	function	✗	✗
max_rows	function	✗	✗
max_rows_increment	function	✗	✗
nbytes	function	✓	✗
equals	function	✓	✗
assert_equals	function	✓	✗
append	function	✓	✗
replace_with	function	✗	✗
clear	function	✓	✗
reset	function	✗	✗
truncate	function	✓	✗
keep_rows	function	✓	✗
copy	function	✓	✗
asdict	function	✓	✗
set_columns	function	✓	✗

Class: MetadataTable

Name	Type	Has Docstring	In Sphinx
MetadataTable	class	✓	✗
packset_metadata	function	✓	✗
metadata_schema	function	✗	✗
metadata_vector	function	✓	✗
drop_metadata	function	✓	✗

Class: IndividualTable

Name	Type	Has Docstring	In Sphinx
IndividualTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓
packset_location	function	✓	✓
packset_parents	function	✓	✓
keep_rows	function	✓	✓

Class: NodeTable

Name	Type	Has Docstring	In Sphinx
NodeTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓

Class: EdgeTable

Name	Type	Has Docstring	In Sphinx
EdgeTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓
squash	function	✓	✓

Class: MigrationTable

Name	Type	Has Docstring	In Sphinx
MigrationTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓

Class: SiteTable

Name	Type	Has Docstring	In Sphinx
SiteTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓
packset_ancestral_state	function	✓	✓

Class: MutationTable

Name	Type	Has Docstring	In Sphinx
MutationTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓
packset_derived_state	function	✓	✓
keep_rows	function	✓	✓

Class: PopulationTable

Name	Type	Has Docstring	In Sphinx
PopulationTable	class	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓

Class: ProvenanceTable

Name	Type	Has Docstring	In Sphinx
ProvenanceTable	class	✓	✓
equals	function	✓	✓
assert_equals	function	✓	✓
add_row	function	✓	✓
set_columns	function	✓	✓
append_columns	function	✓	✓
packset_record	function	✓	✓
packset_timestamp	function	✓	✓

Class: IdentitySegment

Name	Type	Has Docstring	In Sphinx
IdentitySegment	class	✓	✓
span	function	✓	✓

Class: IdentitySegmentList

Name	Type	Has Docstring	In Sphinx
IdentitySegmentList	class	✓	✓
total_span	function	✓	✓
left	function	✓	✓
right	function	✓	✓
node	function	✓	✓

Class: IdentitySegments

Name	Type	Has Docstring	In Sphinx
IdentitySegments	class	✓	✓
num_segments	function	✓	✓
num_pairs	function	✓	✓
total_span	function	✓	✓
pairs	function	✓	✓

Class: ReferenceSequence

Name	Type	Has Docstring	In Sphinx
ReferenceSequence	class	✓	✓
is_null	function	✓	✓
clear	function	✗	✗
data	function	✗	✓
url	function	✗	✗
asdict	function	✗	✗
equals	function	✗	✗
assert_equals	function	✗	✗
nbytes	function	✗	✗

Class: TableCollection

Name	Type	Has Docstring	In Sphinx
TableCollection	class	✓	✓
individuals	function	✗	✓
nodes	function	✗	✓
edges	function	✗	✓
migrations	function	✗	✓
sites	function	✗	✓
mutations	function	✗	✓
populations	function	✗	✓
provenances	function	✗	✓
indexes	function	✗	✓
sequence_length	function	✗	✓
file_uuid	function	✓	✓
time_units	function	✗	✓
has_reference_sequence	function	✓	✓
reference_sequence	function	✗	✓
asdict	function	✓	✓
table_name_map	function	✓	✓
name_map	function	✗	✗
nbytes	function	✓	✓
equals	function	✓	✓
assert_equals	function	✓	✓
load	function	✗	✗
dump	function	✓	✓
fromdict	function	✗	✗
copy	function	✓	✓
tree_sequence	function	✓	✓
simplify	function	✓	✓
link_ancestors	function	✓	✓
map_ancestors	function	✗	✗
sort	function	✓	✓
sort_individuals	function	✓	✓
canonicalise	function	✓	✓
compute_mutation_parents	function	✓	✓
compute_mutation_times	function	✓	✓
deduplicate_sites	function	✓	✓
delete_sites	function	✓	✓
delete_intervals	function	✓	✓
keep_intervals	function	✓	✓
ltrim	function	✓	✓
rtrim	function	✓	✓
trim	function	✓	✓
delete_older	function	✓	✓
clear	function	✓	✓
has_index	function	✓	✓
build_index	function	✓	✓
drop_index	function	✓	✓
subset	function	✓	✓
union	function	✓	✓
ibd_segments	function	✓	✓

Module: exceptions

Isolated Functions

Name	Type	Has Docstring	In Sphinx

Class: DuplicatePositionsError

Name	Type	Has Docstring	In Sphinx
DuplicatePositionsError	class	✓	✗

Class: ProvenanceValidationError

Name	Type	Has Docstring	In Sphinx
ProvenanceValidationError	class	✓	✗

Class: MetadataValidationError

Name	Type	Has Docstring	In Sphinx
MetadataValidationError	class	✓	✗

Class: MetadataSchemaValidationError

Name	Type	Has Docstring	In Sphinx
MetadataSchemaValidationError	class	✓	✗

Class: MetadataEncodingError

Name	Type	Has Docstring	In Sphinx
MetadataEncodingError	class	✓	✗

Module: vcf

Isolated Functions

Name	Type	Has Docstring	In Sphinx
legacy_position_transform	function	✓	✗

Class: VcfWriter

Name	Type	Has Docstring	In Sphinx
VcfWriter	class	✓	✗
write	function	✗	✗