Module tskit::bindings

Expand description

Low-level (“unsafe”) bindings to the C API.

This module is a 1-to-1 mapping of C types and functions for both tskit and kastore. The bindings are generate via bindgen.

Using things from this module will be unsafe. Further, as many of the types require init() methods to correctly set up the structs, one has to coerce rust into allowing uninitialized variables:

use std::mem::MaybeUninit;
let mut edges: MaybeUninit<tskit::bindings::tsk_edge_table_t> = MaybeUninit::uninit();
unsafe {
    let _ = tskit::bindings::tsk_edge_table_init(edges.as_mut_ptr(), 0);
    let _ = tskit::bindings::tsk_edge_table_add_row(edges.as_mut_ptr(), 0., 10., 0, 1, std::ptr::null(), 0);
    assert_eq!((*edges.as_ptr()).num_rows, 1);
    tskit::bindings::tsk_edge_table_free(edges.as_mut_ptr());
}

The best source for documentation will be the tskit docs. Those docs describe the most important parts of the C API. This module contains the same types/functions with the same names.

Structs

_IO_FILE
_IO_codecvt
_IO_marker
_IO_wide_data
_tsk_avl_node_int_t
_tsk_edge_list_node_t
_tsk_identity_segment_t
_tsk_ls_hmm_t
_tsk_table_sorter_t
@brief Low-level table sorting method.
kaitem_t
kastore_t
@brief A file-backed store of key-array values.
tsk_argsort_t
tsk_avl_tree_int_t
tsk_blkalloc_t
tsk_bookmark_t
@brief A bookmark recording the position of all the tables in a table collection.
tsk_compressed_matrix_t
tsk_diff_iter_t
tsk_edge_list_t
tsk_edge_t
@brief A single edge defined by a row in the edge table.
tsk_edge_table_t
@brief The edge table.
tsk_identity_segment_list_t
tsk_identity_segments_t
tsk_individual_t
@brief A single individual defined by a row in the individual table.
tsk_individual_table_t
@brief The individual table.
tsk_ld_calc_t
tsk_migration_t
@brief A single migration defined by a row in the migration table.
tsk_migration_table_t
@brief The migration table.
tsk_mutation_t
@brief A single mutation defined by a row in the mutation table.
tsk_mutation_table_t
@brief The mutation table.
tsk_node_t
@brief A single node defined by a row in the node table.
tsk_node_table_t
@brief The node table.
tsk_population_t
@brief A single population defined by a row in the population table.
tsk_population_table_t
@brief The population table.
tsk_provenance_t
@brief A single provenance defined by a row in the provenance table.
tsk_provenance_table_t
@brief The provenance table.
tsk_recomb_required_record
tsk_reference_sequence_t
tsk_site_probability_t
tsk_site_t
@brief A single site defined by a row in the site table.
tsk_site_table_t
@brief The site table.
tsk_state_transition_t
tsk_table_collection_t
@brief A collection of tables defining the data for a tree sequence.
tsk_table_collection_t__bindgen_ty_1
tsk_transition_stack_t
tsk_tree_t
@brief A single tree in a tree sequence.
tsk_tree_t__bindgen_ty_1
@brief Left and right coordinates of the genomic interval that this tree covers. The left coordinate is inclusive and the right coordinate exclusive.
tsk_treeseq_t
@brief The tree sequence object.
tsk_value_transition_t
tsk_vargen_t
tsk_variant_t
@brief A variant at a specific site.
tsk_viterbi_matrix_t

Constants

Functions

kastore_close^⚠
@brief Close an opened store, freeing all resources.
kastore_contains^⚠
@brief Return 1 if the store contains the specified key and 0 if it does not.
kastore_containss^⚠
@brief Return 1 if the store contains the specified NULL terminated key and 0 if it does not.
kastore_get^⚠
@brief Get the array for the specified key.
kastore_gets^⚠
@brief Get the array for the specified NULL-terminated key.
kastore_gets_float32^⚠
kastore_gets_float64^⚠
kastore_gets_int8^⚠
@defgroup TYPED_GETS_GROUP Typed get functions. @{
kastore_gets_int16^⚠
kastore_gets_int32^⚠
kastore_gets_int64^⚠
kastore_gets_uint8^⚠
kastore_gets_uint16^⚠
kastore_gets_uint32^⚠
kastore_gets_uint64^⚠
kastore_open^⚠
@brief Open a store from a given file in read (“r”), write (“w”) or append (“a”) mode.
kastore_openf^⚠
@brief Open a store from a given FILE pointer.
kastore_oput^⚠
@brief Insert the specified key-array pair into the store, transferring ownership of the malloced array buffer to the store (own-put).
kastore_oputs^⚠
@brief Insert the specified NULL terminated key and array pair into the store, transferring ownership of the malloced array buffer to the store (own-put).
kastore_oputs_float32^⚠
kastore_oputs_float64^⚠
kastore_oputs_int8^⚠
@defgroup TYPED_OPUTS_GROUP Typed own-and-put functions. @{
kastore_oputs_int16^⚠
kastore_oputs_int32^⚠
kastore_oputs_int64^⚠
kastore_oputs_uint8^⚠
kastore_oputs_uint16^⚠
kastore_oputs_uint32^⚠
kastore_oputs_uint64^⚠
kastore_print_state^⚠
@}
kastore_put^⚠
@brief Insert the specified key-array pair into the store.
kastore_puts^⚠
@brief Insert the specified NULL terminated key and array pair into the store.
kastore_puts_float32^⚠
kastore_puts_float64^⚠
kastore_puts_int8^⚠
@defgroup TYPED_PUTS_GROUP Typed put functions. @{
kastore_puts_int16^⚠
kastore_puts_int32^⚠
kastore_puts_int64^⚠
kastore_puts_uint8^⚠
kastore_puts_uint16^⚠
kastore_puts_uint32^⚠
kastore_puts_uint64^⚠
tsk_avl_tree_int_free^⚠
tsk_avl_tree_int_get_root^⚠
tsk_avl_tree_int_init^⚠
tsk_avl_tree_int_insert^⚠
tsk_avl_tree_int_ordered_nodes^⚠
tsk_avl_tree_int_print_state^⚠
tsk_avl_tree_int_search^⚠
tsk_blkalloc_free^⚠
tsk_blkalloc_get^⚠
tsk_blkalloc_init^⚠
tsk_blkalloc_print_state^⚠
tsk_blkalloc_reset^⚠
tsk_calloc^⚠
tsk_compressed_matrix_clear^⚠
tsk_compressed_matrix_decode^⚠
tsk_compressed_matrix_free^⚠
tsk_compressed_matrix_init^⚠
tsk_compressed_matrix_print_state^⚠
tsk_compressed_matrix_store_site^⚠
tsk_convert_newick^⚠
tsk_diff_iter_free^⚠
tsk_diff_iter_init^⚠
tsk_diff_iter_next^⚠
tsk_diff_iter_print_state^⚠
tsk_edge_table_add_row^⚠
@brief Adds a row to this edge table.
tsk_edge_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_edge_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_edge_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_edge_table_dump_text^⚠
@}
tsk_edge_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_edge_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_edge_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_edge_table_get_row^⚠
@brief Get the row at the specified index.
tsk_edge_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_edge_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_edge_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_edge_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_edge_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_edge_table_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table, replacing any existing. @endrst @param self A pointer to a tsk_edge_table_t object. @param metadata_schema A pointer to a char array @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_edge_table_squash^⚠
@brief Squash adjacent edges in-place
tsk_edge_table_takeset_columns^⚠
tsk_edge_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_edge_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_generate_uuid^⚠
tsk_get_debug_stream^⚠
tsk_get_kas_error^⚠
tsk_identity_segments_free^⚠
tsk_identity_segments_get^⚠
tsk_identity_segments_get_items^⚠
tsk_identity_segments_get_keys^⚠
tsk_identity_segments_get_num_pairs^⚠
tsk_identity_segments_get_num_segments^⚠
tsk_identity_segments_get_total_span^⚠
tsk_identity_segments_print_state^⚠
tsk_individual_table_add_row^⚠
@brief Adds a row to this individual table.
tsk_individual_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_individual_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_individual_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_individual_table_dump_text^⚠
@}
tsk_individual_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_individual_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_individual_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_individual_table_get_row^⚠
@brief Get the row at the specified index.
tsk_individual_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_individual_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_individual_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_individual_table_set_max_location_length_increment^⚠
@brief Controls the pre-allocation strategy for the location column
tsk_individual_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_individual_table_set_max_parents_length_increment^⚠
@brief Controls the pre-allocation strategy for the parents column
tsk_individual_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_individual_table_set_metadata_schema^⚠
@brief Set the metadata schema
tsk_individual_table_takeset_columns^⚠
tsk_individual_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_individual_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_is_kas_error^⚠
tsk_is_unknown_time^⚠
@brief Check if a number is TSK_UNKNOWN_TIME
tsk_isfinite^⚠
tsk_isnan^⚠
tsk_ld_calc_free^⚠
tsk_ld_calc_get_r2^⚠
tsk_ld_calc_get_r2_array^⚠
tsk_ld_calc_init^⚠
tsk_ld_calc_print_state^⚠
tsk_ls_hmm_forward^⚠
tsk_ls_hmm_free^⚠
tsk_ls_hmm_init^⚠
tsk_ls_hmm_print_state^⚠
tsk_ls_hmm_run^⚠
tsk_ls_hmm_set_precision^⚠
tsk_ls_hmm_viterbi^⚠
tsk_malloc^⚠
tsk_memcmp^⚠
tsk_memcpy^⚠
tsk_memmove^⚠
tsk_memset^⚠
tsk_migration_table_add_row^⚠
@brief Adds a row to this migration table.
tsk_migration_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_migration_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_migration_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_migration_table_dump_text^⚠
@}
tsk_migration_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_migration_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_migration_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_migration_table_get_row^⚠
@brief Get the row at the specified index.
tsk_migration_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_migration_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_migration_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_migration_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_migration_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_migration_table_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table, replacing any existing. @endrst @param self A pointer to a tsk_migration_table_t object. @param metadata_schema A pointer to a char array. @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_migration_table_takeset_columns^⚠
tsk_migration_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_migration_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_mutation_table_add_row^⚠
@brief Adds a row to this mutation table.
tsk_mutation_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_mutation_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_mutation_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_mutation_table_dump_text^⚠
@}
tsk_mutation_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_mutation_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_mutation_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_mutation_table_get_row^⚠
@brief Get the row at the specified index.
tsk_mutation_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_mutation_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_mutation_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_mutation_table_set_max_derived_state_length_increment^⚠
@brief Controls the pre-allocation strategy for the derived_state column
tsk_mutation_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_mutation_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_mutation_table_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table, replacing any existing. @endrst @param self A pointer to a tsk_mutation_table_t object. @param metadata_schema A pointer to a char array. @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_mutation_table_takeset_columns^⚠
tsk_mutation_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_mutation_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_node_table_add_row^⚠
@brief Adds a row to this node table.
tsk_node_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_node_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_node_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_node_table_dump_text^⚠
@}
tsk_node_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_node_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_node_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_node_table_get_row^⚠
@brief Get the row at the specified index.
tsk_node_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_node_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_node_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_node_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_node_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_node_table_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table, replacing any existing. @endrst @param self A pointer to a tsk_node_table_t object. @param metadata_schema A pointer to a char array. @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_node_table_takeset_columns^⚠
tsk_node_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_node_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_population_table_add_row^⚠
@brief Adds a row to this population table.
tsk_population_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_population_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_population_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_population_table_dump_text^⚠
@}
tsk_population_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_population_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_population_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_population_table_get_row^⚠
@brief Get the row at the specified index.
tsk_population_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_population_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_population_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_population_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_population_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_population_table_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table, replacing any existing. @endrst @param self A pointer to a tsk_population_table_t object. @param metadata_schema A pointer to a char array. @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_population_table_takeset_columns^⚠
tsk_population_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_population_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_provenance_table_add_row^⚠
@brief Adds a row to this provenance table.
tsk_provenance_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_provenance_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_provenance_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_provenance_table_dump_text^⚠
@}
tsk_provenance_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_provenance_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_provenance_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_provenance_table_get_row^⚠
@brief Get the row at the specified index.
tsk_provenance_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_provenance_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_provenance_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_provenance_table_set_max_record_length_increment^⚠
@brief Controls the pre-allocation strategy for the record column
tsk_provenance_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_provenance_table_set_max_timestamp_length_increment^⚠
@brief Controls the pre-allocation strategy for the timestamp column
tsk_provenance_table_takeset_columns^⚠
tsk_provenance_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_provenance_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_realloc^⚠
tsk_reference_sequence_copy^⚠
tsk_reference_sequence_equals^⚠
tsk_reference_sequence_free^⚠
tsk_reference_sequence_init^⚠
tsk_reference_sequence_is_null^⚠
tsk_reference_sequence_set_data^⚠
tsk_reference_sequence_set_metadata^⚠
tsk_reference_sequence_set_metadata_schema^⚠
tsk_reference_sequence_set_url^⚠
tsk_reference_sequence_takeset_data^⚠
tsk_reference_sequence_takeset_metadata^⚠
tsk_round^⚠
tsk_search_sorted^⚠
tsk_set_debug_stream^⚠
tsk_set_kas_error^⚠
tsk_site_table_add_row^⚠
@brief Adds a row to this site table.
tsk_site_table_append_columns^⚠
@brief Extends this table by copying from a set of column arrays
tsk_site_table_clear^⚠
@brief Clears this table, setting the number of rows to zero.
tsk_site_table_copy^⚠
@brief Copies the state of this table into the specified destination.
tsk_site_table_dump_text^⚠
@}
tsk_site_table_equals^⚠
@brief Returns true if the data in the specified table is identical to the data in this table.
tsk_site_table_extend^⚠
@brief Extends this table by appending rows copied from another table.
tsk_site_table_free^⚠
@brief Free the internal memory for the specified table.
tsk_site_table_get_row^⚠
@brief Get the row at the specified index.
tsk_site_table_init^⚠
@brief Initialises the table by allocating the internal memory.
tsk_site_table_print_state^⚠
@brief Print out the state of this table to the specified stream.
tsk_site_table_set_columns^⚠
@brief Replace this table’s data by copying from a set of column arrays
tsk_site_table_set_max_ancestral_state_length_increment^⚠
@brief Controls the pre-allocation strategy for the ancestral_state column
tsk_site_table_set_max_metadata_length_increment^⚠
@brief Controls the pre-allocation strategy for the metadata column
tsk_site_table_set_max_rows_increment^⚠
@brief Controls the pre-allocation strategy for this table
tsk_site_table_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table, replacing any existing. @endrst @param self A pointer to a tsk_site_table_t object. @param metadata_schema A pointer to a char array. @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_site_table_takeset_columns^⚠
tsk_site_table_truncate^⚠
@brief Truncates this table so that only the first num_rows are retained.
tsk_site_table_update_row^⚠
@brief Updates the row at the specified index.
tsk_squash_edges^⚠
@}
tsk_strerror^⚠
@brief Return a description of the specified error.
tsk_table_collection_build_index^⚠
@brief Builds indexes for this table collection.
tsk_table_collection_canonicalise^⚠
@brief Puts the tables into canonical form.
tsk_table_collection_check_integrity^⚠
@brief Runs integrity checks on this table collection.
tsk_table_collection_clear^⚠
@brief Clears data tables (and optionally provenances and metadata) in this table collection.
tsk_table_collection_compute_mutation_parents^⚠
tsk_table_collection_compute_mutation_times^⚠
tsk_table_collection_copy^⚠
@brief Copies the state of this table collection into the specified destination.
tsk_table_collection_deduplicate_sites^⚠
tsk_table_collection_delete_older^⚠
tsk_table_collection_drop_index^⚠
@brief Deletes the indexes for this table collection.
tsk_table_collection_dump^⚠
@brief Write a table collection to file.
tsk_table_collection_dumpf^⚠
@brief Write a table collection to a stream.
tsk_table_collection_equals^⚠
@brief Returns true if the data in the specified table collection is equal to the data in this table collection.
tsk_table_collection_free^⚠
@brief Free the internal memory for the specified table collection.
tsk_table_collection_has_index^⚠
@brief Returns true if this table collection is indexed.
tsk_table_collection_has_reference_sequence^⚠
tsk_table_collection_ibd_between^⚠
tsk_table_collection_ibd_within^⚠
tsk_table_collection_individual_topological_sort^⚠
@brief Sorts the individual table in this collection.
tsk_table_collection_init^⚠
@brief Initialises the table collection by allocating the internal memory and initialising all the constituent tables.
tsk_table_collection_link_ancestors^⚠
tsk_table_collection_load^⚠
@brief Load a table collection from a file path.
tsk_table_collection_loadf^⚠
@brief Load a table collection from a stream.
tsk_table_collection_print_state^⚠
@brief Print out the state of this table collection to the specified stream.
tsk_table_collection_record_num_rows^⚠
@brief Record the number of rows in each table in the specified tsk_bookmark_t object.
tsk_table_collection_set_indexes^⚠
tsk_table_collection_set_metadata^⚠
@brief Set the metadata @rst Copies the metadata string to this table collection, replacing any existing. @endrst @param self A pointer to a tsk_table_collection_t object. @param metadata A pointer to a char array. @param metadata_length The size of the metadata in bytes. @return Return 0 on success or a negative value on failure.
tsk_table_collection_set_metadata_schema^⚠
@brief Set the metadata schema @rst Copies the metadata schema string to this table collection, replacing any existing. @endrst @param self A pointer to a tsk_table_collection_t object. @param metadata_schema A pointer to a char array. @param metadata_schema_length The size of the metadata schema in bytes. @return Return 0 on success or a negative value on failure.
tsk_table_collection_set_time_units^⚠
@brief Set the time_units @rst Copies the time_units string to this table collection, replacing any existing. @endrst @param self A pointer to a tsk_table_collection_t object. @param time_units A pointer to a char array. @param time_units_length The size of the time units string in bytes. @return Return 0 on success or a negative value on failure.
tsk_table_collection_simplify^⚠
@brief Simplify the tables to remove redundant information.
tsk_table_collection_sort^⚠
@brief Sorts the tables in this collection.
tsk_table_collection_subset^⚠
@brief Subsets and reorders a table collection according to an array of nodes.
tsk_table_collection_takeset_indexes^⚠
tsk_table_collection_takeset_metadata^⚠
tsk_table_collection_truncate^⚠
@brief Truncates the tables in this table collection according to the specified bookmark.
tsk_table_collection_union^⚠
@brief Forms the node-wise union of two table collections.
tsk_table_sorter_free^⚠
@brief Free the internal memory for the specified table sorter.
tsk_table_sorter_init^⚠
@brief Initialises the memory for the sorter object.
tsk_table_sorter_run^⚠
@brief Runs the sort using the configured functions.
tsk_tree_b1_index^⚠
tsk_tree_b2_index^⚠
tsk_tree_clear^⚠
@brief Set the tree into the null state.
tsk_tree_colless_index^⚠
tsk_tree_copy^⚠
@brief Copies the state of this tree into the specified destination.
tsk_tree_equals^⚠
tsk_tree_first^⚠
@brief Seek to the first tree in the sequence.
tsk_tree_free^⚠
@brief Free the internal memory for the specified tree.
tsk_tree_get_branch_length^⚠
@brief Return the length of the branch ancestral to the specified node.
tsk_tree_get_depth^⚠
@brief Return number of nodes on the path from the specified node to root.
tsk_tree_get_left_root^⚠
@brief Returns the leftmost root in this tree.
tsk_tree_get_mrca^⚠
@brief Compute the most recent common ancestor of two nodes.
tsk_tree_get_num_roots^⚠
@brief Returns the number of roots in this tree.
tsk_tree_get_num_samples^⚠
@brief Counts the number of samples in the subtree rooted at a node.
tsk_tree_get_num_tracked_samples^⚠
tsk_tree_get_parent^⚠
@brief Returns the parent of the specified node.
tsk_tree_get_right_root^⚠
@brief Returns the rightmost root in this tree.
tsk_tree_get_root_threshold^⚠
tsk_tree_get_sites^⚠
@brief Get the list of sites for this tree.
tsk_tree_get_size_bound^⚠
@brief Return an upper bound on the number of nodes reachable from the roots of this tree.
tsk_tree_get_time^⚠
@brief Returns the time of the specified node.
tsk_tree_get_total_branch_length^⚠
@brief Computes the sum of the lengths of all branches reachable from the specified node, or from all roots if u=TSK_NULL.
tsk_tree_has_sample_counts^⚠
tsk_tree_has_sample_lists^⚠
tsk_tree_init^⚠
@brief Initialises the tree by allocating internal memory and associating with the specified tree sequence.
tsk_tree_is_descendant^⚠
@brief Returns true if u is a descendant of v.
tsk_tree_is_sample^⚠
tsk_tree_kc_distance^⚠
tsk_tree_last^⚠
@brief Seek to the last tree in the sequence.
tsk_tree_map_mutations^⚠
tsk_tree_next^⚠
@brief Seek to the next tree in the sequence.
tsk_tree_num_lineages^⚠
tsk_tree_postorder^⚠
@brief Fill an array with the nodes of this tree in postorder.
tsk_tree_postorder_from^⚠
@brief Fill an array with the nodes of this tree starting from a particular node.
tsk_tree_preorder^⚠
@brief Fill an array with the nodes of this tree in preorder.
tsk_tree_preorder_from^⚠
@brief Fill an array with the nodes of this tree starting from a particular node.
tsk_tree_preorder_samples_from^⚠
@}
tsk_tree_prev^⚠
@brief Seek to the previous tree in the sequence.
tsk_tree_print_state^⚠
@brief Print out the state of this tree to the specified stream.
tsk_tree_sackin_index^⚠
tsk_tree_seek^⚠
@brief Seek to a particular position on the genome.
tsk_tree_set_root_threshold^⚠
tsk_tree_set_tracked_samples^⚠
tsk_tree_track_descendant_samples^⚠
tsk_treeseq_Y1^⚠
tsk_treeseq_Y2^⚠
tsk_treeseq_Y3^⚠
tsk_treeseq_allele_frequency_spectrum^⚠
tsk_treeseq_copy_tables^⚠
@brief Copies the state of the table collection underlying this tree sequence into the specified destination table collection.
tsk_treeseq_divergence^⚠
tsk_treeseq_diversity^⚠
tsk_treeseq_dump^⚠
@brief Write a tree sequence to file.
tsk_treeseq_dumpf^⚠
@brief Write a tree sequence to a stream.
tsk_treeseq_f2^⚠
tsk_treeseq_f3^⚠
tsk_treeseq_f4^⚠
tsk_treeseq_free^⚠
@brief Free the internal memory for the specified tree sequence.
tsk_treeseq_genealogical_nearest_neighbours^⚠
tsk_treeseq_general_stat^⚠
tsk_treeseq_genetic_relatedness^⚠
tsk_treeseq_get_breakpoints^⚠
@brief Get the breakpoints
tsk_treeseq_get_discrete_genome^⚠
@brief Get the discrete genome status
tsk_treeseq_get_discrete_time^⚠
@brief Get the discrete time status
tsk_treeseq_get_edge^⚠
@brief Get a edge by its index
tsk_treeseq_get_file_uuid^⚠
@brief Get the file uuid
tsk_treeseq_get_individual^⚠
@brief Get a individual by its index
tsk_treeseq_get_individuals_population^⚠
tsk_treeseq_get_individuals_time^⚠
tsk_treeseq_get_metadata^⚠
@brief Get the top-level tree sequence metadata.
tsk_treeseq_get_metadata_length^⚠
@brief Get the length of top-level tree sequence metadata
tsk_treeseq_get_metadata_schema^⚠
@brief Get the top-level tree sequence metadata schema.
tsk_treeseq_get_metadata_schema_length^⚠
@brief Get the length of the top-level tree sequence metadata schema.
tsk_treeseq_get_migration^⚠
@brief Get a edge by its index
tsk_treeseq_get_mutation^⚠
@brief Get a mutation by its index
tsk_treeseq_get_node^⚠
@brief Get a node by its index
tsk_treeseq_get_num_edges^⚠
@brief Get the number of edges
tsk_treeseq_get_num_individuals^⚠
@brief Get the number of individuals
tsk_treeseq_get_num_migrations^⚠
@brief Get the number of migrations
tsk_treeseq_get_num_mutations^⚠
@brief Get the number of mutations
tsk_treeseq_get_num_nodes^⚠
@brief Get the number of nodes
tsk_treeseq_get_num_populations^⚠
@brief Get the number of populations
tsk_treeseq_get_num_provenances^⚠
@brief Get the number of provenances
tsk_treeseq_get_num_samples^⚠
@brief Get the number of samples
tsk_treeseq_get_num_sites^⚠
@brief Get the number of sites
tsk_treeseq_get_num_trees^⚠
@brief Return the number of trees in this tree sequence.
tsk_treeseq_get_population^⚠
@brief Get a population by its index
tsk_treeseq_get_provenance^⚠
@brief Get a provenance by its index
tsk_treeseq_get_sample_index_map^⚠
@brief Get the map of node id to sample index
tsk_treeseq_get_samples^⚠
@brief Get the samples
tsk_treeseq_get_sequence_length^⚠
@brief Get the sequence length
tsk_treeseq_get_site^⚠
@brief Get a site by its index
tsk_treeseq_get_time_units^⚠
@brief Get the time units string
tsk_treeseq_get_time_units_length^⚠
@brief Get the length of time units string @rst Returns the length of the time units string. @endrst
tsk_treeseq_has_reference_sequence^⚠
tsk_treeseq_init^⚠
@brief Initialises the tree sequence based on the specified table collection.
tsk_treeseq_is_sample^⚠
@brief Check if a node is a sample
tsk_treeseq_kc_distance^⚠
tsk_treeseq_load^⚠
@brief Load a tree sequence from a file path.
tsk_treeseq_loadf^⚠
@brief Load a tree sequence from a stream.
tsk_treeseq_mean_descendants^⚠
tsk_treeseq_print_state^⚠
@brief Print out the state of this tree sequence to the specified stream.
tsk_treeseq_segregating_sites^⚠
tsk_treeseq_simplify^⚠
@brief Create a simplified instance of this tree sequence
tsk_treeseq_split_edges^⚠
@}
tsk_treeseq_trait_correlation^⚠
tsk_treeseq_trait_covariance^⚠
tsk_treeseq_trait_linear_model^⚠
tsk_vargen_free^⚠
tsk_vargen_init^⚠
@}
tsk_vargen_next^⚠
tsk_vargen_print_state^⚠
tsk_variant_decode^⚠
@brief Decode the genotypes at the given site, storing them in this variant.
tsk_variant_free^⚠
@brief Free the internal memory for the specified variant.
tsk_variant_init^⚠
@brief Initialises the variant by allocating the internal memory
tsk_variant_print_state^⚠
@brief Print out the state of this variant to the specified stream.
tsk_variant_restricted_copy^⚠
@brief Copies the state of this variant to another variant
tsk_viterbi_matrix_add_recombination_required^⚠
tsk_viterbi_matrix_clear^⚠
tsk_viterbi_matrix_free^⚠
tsk_viterbi_matrix_init^⚠
tsk_viterbi_matrix_print_state^⚠
tsk_viterbi_matrix_traceback^⚠

Type Definitions

FILE
_IO_lock_t
__off64_t
__off_t
general_stat_func_t
tsk_avl_node_int_t
tsk_edge_list_node_t
tsk_flags_t
@brief Container for bitwise flags.
tsk_id_t
tsk_identity_segment_t
tsk_ls_hmm_t
tsk_size_t
@brief Tskit sizes.
tsk_table_sorter_t
@brief Low-level table sorting method.