Module bindings

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

KAS_ARRAY_ALIGN

KAS_BORROWS_ARRAY

KAS_BUG_ASSERT_MESSAGE

KAS_ERR_BAD_FILE_FORMAT

KAS_ERR_BAD_FLAGS

KAS_ERR_BAD_MODE

KAS_ERR_BAD_TYPE

KAS_ERR_DUPLICATE_KEY

KAS_ERR_EMPTY_KEY

KAS_ERR_EOF

KAS_ERR_GENERIC

KAS_ERR_ILLEGAL_OPERATION

KAS_ERR_IO

KAS_ERR_KEY_NOT_FOUND

KAS_ERR_NO_MEMORY

KAS_ERR_TYPE_MISMATCH

KAS_ERR_VERSION_TOO_NEW

KAS_ERR_VERSION_TOO_OLD

KAS_FILE_VERSION_MAJOR

KAS_FILE_VERSION_MINOR

KAS_FLOAT32

KAS_FLOAT64

KAS_GET_TAKES_OWNERSHIP

KAS_HEADER_SIZE

KAS_INT8

KAS_INT16

KAS_INT32

KAS_INT64

KAS_ITEM_DESCRIPTOR_SIZE

KAS_MAGIC

KAS_NUM_TYPES

KAS_READ

KAS_READ_ALL

KAS_UINT8

KAS_UINT16

KAS_UINT32

KAS_UINT64

KAS_VERSION_MAJOR

KAS_VERSION_MINOR

KAS_VERSION_PATCH

KAS_WRITE

TSK_ALLELES_ACGT

TSK_BUG_ASSERT_MESSAGE

TSK_CHECK_EDGE_ORDERING

TSK_CHECK_INDEXES

TSK_CHECK_INDIVIDUAL_ORDERING

TSK_CHECK_MIGRATION_ORDERING

TSK_CHECK_MUTATION_ORDERING

TSK_CHECK_SITE_DUPLICATES

TSK_CHECK_SITE_ORDERING

TSK_CHECK_TREES

TSK_CLEAR_METADATA_SCHEMAS

TSK_CLEAR_PROVENANCE

TSK_CLEAR_TS_METADATA_AND_SCHEMA

TSK_CMP_IGNORE_METADATA

TSK_CMP_IGNORE_PROVENANCE

TSK_CMP_IGNORE_REFERENCE_SEQUENCE

TSK_CMP_IGNORE_TABLES

TSK_CMP_IGNORE_TIMESTAMPS

TSK_CMP_IGNORE_TS_METADATA

TSK_COPY_FILE_UUID

TSK_DEBUG

TSK_DIR_FORWARD

TSK_DIR_REVERSE

TSK_DUMP_FORCE_OFFSET_64

TSK_ERR_ALLELE_NOT_FOUND

TSK_ERR_BAD_ANCESTRAL_STATE

TSK_ERR_BAD_COLUMN_TYPE

TSK_ERR_BAD_COMPRESSED_MATRIX_NODE

TSK_ERR_BAD_EDGES_CONTRADICTORY_CHILDREN

TSK_ERR_BAD_EDGE_INTERVAL

TSK_ERR_BAD_GENOTYPE

TSK_ERR_BAD_NODE_TIME_ORDERING

TSK_ERR_BAD_NUM_WINDOWS

TSK_ERR_BAD_OFFSET

TSK_ERR_BAD_PARAM_VALUE

TSK_ERR_BAD_RESULT_DIMS

TSK_ERR_BAD_SAMPLES

TSK_ERR_BAD_SAMPLE_SET_INDEX

TSK_ERR_BAD_SEQUENCE_LENGTH

TSK_ERR_BAD_SITE_POSITION

TSK_ERR_BAD_STATE_DIMS

TSK_ERR_BAD_TABLE_POSITION

TSK_ERR_BAD_WINDOWS

TSK_ERR_BOTH_COLUMNS_REQUIRED

TSK_ERR_BUFFER_OVERFLOW

TSK_ERR_CANNOT_EXTEND_FROM_SELF

TSK_ERR_CANT_PROCESS_EDGES_WITH_METADATA

TSK_ERR_CANT_TAKE_OWNERSHIP_NO_EDGE_METADATA

TSK_ERR_COLUMN_OVERFLOW

TSK_ERR_DUPLICATE_EDGES

TSK_ERR_DUPLICATE_SAMPLE

TSK_ERR_DUPLICATE_SITE_POSITION

TSK_ERR_EDGES_NONCONTIGUOUS_PARENTS

TSK_ERR_EDGES_NOT_SORTED_CHILD

TSK_ERR_EDGES_NOT_SORTED_LEFT

TSK_ERR_EDGES_NOT_SORTED_PARENT_TIME

TSK_ERR_EDGE_OUT_OF_BOUNDS

TSK_ERR_EMPTY_SAMPLE_SET

TSK_ERR_EOF

TSK_ERR_FILE_FORMAT

TSK_ERR_FILE_VERSION_TOO_NEW

TSK_ERR_FILE_VERSION_TOO_OLD

TSK_ERR_GENERATE_UUID

TSK_ERR_GENERIC

TSK_ERR_GENOME_COORDS_NONFINITE

TSK_ERR_GENOTYPES_ALL_MISSING

TSK_ERR_IBD_PAIRS_NOT_STORED

TSK_ERR_IBD_SEGMENTS_NOT_STORED

TSK_ERR_INDIVIDUAL_OUT_OF_BOUNDS

TSK_ERR_INDIVIDUAL_PARENT_CYCLE

TSK_ERR_INDIVIDUAL_POPULATION_MISMATCH

TSK_ERR_INDIVIDUAL_SELF_PARENT

TSK_ERR_INDIVIDUAL_TIME_MISMATCH

TSK_ERR_INSUFFICIENT_INDEX_TUPLES

TSK_ERR_INSUFFICIENT_SAMPLE_SETS

TSK_ERR_IO

TSK_ERR_KEEP_UNARY_MUTUALLY_EXCLUSIVE

TSK_ERR_LEFT_LESS_ZERO

TSK_ERR_MATCH_IMPOSSIBLE

TSK_ERR_METADATA_DISABLED

TSK_ERR_MIGRATIONS_NOT_SUPPORTED

TSK_ERR_MIGRATION_OUT_OF_BOUNDS

TSK_ERR_MULTIPLE_ROOTS

TSK_ERR_MULTIPLE_STAT_MODES

TSK_ERR_MUST_IMPUTE_NON_SAMPLES

TSK_ERR_MUTATION_OUT_OF_BOUNDS

TSK_ERR_MUTATION_PARENT_AFTER_CHILD

TSK_ERR_MUTATION_PARENT_DIFFERENT_SITE

TSK_ERR_MUTATION_PARENT_EQUAL

TSK_ERR_MUTATION_PARENT_INCONSISTENT

TSK_ERR_MUTATION_TIME_HAS_BOTH_KNOWN_AND_UNKNOWN

TSK_ERR_MUTATION_TIME_OLDER_THAN_PARENT_MUTATION

TSK_ERR_MUTATION_TIME_OLDER_THAN_PARENT_NODE

TSK_ERR_MUTATION_TIME_YOUNGER_THAN_NODE

TSK_ERR_NODE_OUT_OF_BOUNDS

TSK_ERR_NONBINARY_MUTATIONS_UNSUPPORTED

TSK_ERR_NO_MEMORY

TSK_ERR_NO_SAMPLE_LISTS

TSK_ERR_NULL_CHILD

TSK_ERR_NULL_PARENT

TSK_ERR_NULL_VITERBI_MATRIX

TSK_ERR_ONLY_INFINITE_SITES

TSK_ERR_POPULATION_OUT_OF_BOUNDS

TSK_ERR_PROVENANCE_OUT_OF_BOUNDS

TSK_ERR_REQUIRED_COL_NOT_FOUND

TSK_ERR_RIGHT_GREATER_SEQ_LENGTH

TSK_ERR_SAME_NODES_IN_PAIR

TSK_ERR_SAMPLES_NOT_EQUAL

TSK_ERR_SAMPLE_SIZE_MISMATCH

TSK_ERR_SEEK_OUT_OF_BOUNDS

TSK_ERR_SEQUENCE_LENGTH_MISMATCH

TSK_ERR_SILENT_MUTATIONS_NOT_SUPPORTED

TSK_ERR_SIMPLIFY_MIGRATIONS_NOT_SUPPORTED

TSK_ERR_SITE_OUT_OF_BOUNDS

TSK_ERR_SORT_MIGRATIONS_NOT_SUPPORTED

TSK_ERR_SORT_OFFSET_NOT_SUPPORTED

TSK_ERR_TABLES_BAD_INDEXES

TSK_ERR_TABLES_NOT_INDEXED

TSK_ERR_TABLE_OVERFLOW

TSK_ERR_TIME_NONFINITE

TSK_ERR_TIME_UNCALIBRATED

TSK_ERR_TOO_MANY_ALLELES

TSK_ERR_TOO_MANY_VALUES

TSK_ERR_TREE_OVERFLOW

TSK_ERR_UNARY_NODES

TSK_ERR_UNDEFINED_MULTIROOT

TSK_ERR_UNDEFINED_NONBINARY

TSK_ERR_UNION_BAD_MAP

TSK_ERR_UNION_DIFF_HISTORIES

TSK_ERR_UNSORTED_INDIVIDUALS

TSK_ERR_UNSORTED_MIGRATIONS

TSK_ERR_UNSORTED_MUTATIONS

TSK_ERR_UNSORTED_SITES

TSK_ERR_UNSUPPORTED_OPERATION

TSK_ERR_UNSUPPORTED_STAT_MODE

TSK_ERR_VARIANT_CANT_DECODE_COPY

TSK_ERR_ZERO_ALLELES

TSK_FILE_FORMAT_NAME

TSK_FILE_FORMAT_NAME_LENGTH

TSK_FILE_FORMAT_VERSION_MAJOR

TSK_FILE_FORMAT_VERSION_MINOR

TSK_IBD_STORE_PAIRS

TSK_IBD_STORE_SEGMENTS

TSK_INCLUDE_TERMINAL

TSK_ISOLATED_NOT_MISSING

TSK_KAS_ERR_BIT

TSK_LOAD_SKIP_REFERENCE_SEQUENCE

TSK_LOAD_SKIP_TABLES

TSK_MAX_ID

TSK_MISSING_DATA

TSK_MM_FIXED_ANCESTRAL_STATE

TSK_NEWICK_LEGACY_MS_LABELS

TSK_NODE_IS_SAMPLE

TSK_NO_CHECK_INTEGRITY

TSK_NO_CHECK_POPULATION_REFS

TSK_NO_INIT

TSK_NO_SAMPLE_COUNTS

TSK_SAMPLE_LISTS

TSK_SIMPLIFY_FILTER_INDIVIDUALS

TSK_SIMPLIFY_FILTER_POPULATIONS

TSK_SIMPLIFY_FILTER_SITES

TSK_SIMPLIFY_KEEP_INPUT_ROOTS

TSK_SIMPLIFY_KEEP_UNARY

TSK_SIMPLIFY_KEEP_UNARY_IN_INDIVIDUALS

TSK_SIMPLIFY_REDUCE_TO_SITE_TOPOLOGY

TSK_STAT_ALLOW_TIME_UNCALIBRATED

TSK_STAT_BRANCH

TSK_STAT_NODE

TSK_STAT_POLARISED

TSK_STAT_SITE

TSK_STAT_SPAN_NORMALISE

TSK_SUBSET_KEEP_UNREFERENCED

TSK_SUBSET_NO_CHANGE_POPULATIONS

TSK_TABLE_NO_METADATA

TSK_TAKE_OWNERSHIP

TSK_TC_NO_EDGE_METADATA

TSK_TIME_UNITS_UNCALIBRATED

TSK_TIME_UNITS_UNKNOWN

TSK_TREE_OK

TSK_TS_INIT_BUILD_INDEXES

TSK_UNION_NO_ADD_POP

TSK_UNION_NO_CHECK_SHARED

TSK_UNKNOWN_TIME_HEX

TSK_UUID_SIZE

TSK_VERSION_MAJOR

TSK_VERSION_MINOR

TSK_VERSION_PATCH

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 Aliases

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.