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
@brief Low-level table sorting method.
@brief A file-backed store of key-array values.
@brief A bookmark recording the position of all the tables in a table collection.
@brief A single edge defined by a row in the edge table.
@brief The edge table.
@brief A single individual defined by a row in the individual table.
@brief The individual table.
@brief A single migration defined by a row in the migration table.
@brief The migration table.
@brief A single mutation defined by a row in the mutation table.
@brief The mutation table.
@brief A single node defined by a row in the node table.
@brief The node table.
@brief A single population defined by a row in the population table.
@brief The population table.
@brief A single provenance defined by a row in the provenance table.
@brief The provenance table.
@brief A single site defined by a row in the site table.
@brief The site table.
@brief A collection of tables defining the data for a tree sequence.
@brief A single tree in a tree sequence.
@brief Left and right coordinates of the genomic interval that this tree covers. The left coordinate is inclusive and the right coordinate exclusive.
@brief The tree sequence object.
@brief A variant at a specific site.
Constants
Functions
@brief Close an opened store, freeing all resources.
@brief Return 1 if the store contains the specified key and 0 if it does not.
@brief Return 1 if the store contains the specified NULL terminated key and 0 if it does not.
@brief Get the array for the specified key.
@brief Get the array for the specified NULL-terminated key.
@defgroup TYPED_GETS_GROUP Typed get functions. @{
@brief Open a store from a given file in read (“r”), write (“w”) or append (“a”) mode.
@brief Open a store from a given FILE pointer.
@brief Insert the specified key-array pair into the store, transferring ownership of the malloced array buffer to the store (own-put).
@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).
@defgroup TYPED_OPUTS_GROUP Typed own-and-put functions. @{
@brief Insert the specified key-array pair into the store.
@brief Insert the specified NULL terminated key and array pair into the store.
@defgroup TYPED_PUTS_GROUP Typed put functions. @{
@brief Adds a row to this edge table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for this table
@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.
@brief Squash adjacent edges in-place
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Adds a row to this individual table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the location column
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for the parents column
@brief Controls the pre-allocation strategy for this table
@brief Set the metadata schema
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Check if a number is TSK_UNKNOWN_TIME
@brief Adds a row to this migration table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for this table
@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.
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Adds a row to this mutation table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the derived_state column
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for this table
@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.
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Adds a row to this node table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for this table
@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.
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Adds a row to this population table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for this table
@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.
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Adds a row to this provenance table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the record column
@brief Controls the pre-allocation strategy for this table
@brief Controls the pre-allocation strategy for the timestamp column
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Adds a row to this site table.
@brief Extends this table by copying from a set of column arrays
@brief Clears this table, setting the number of rows to zero.
@brief Copies the state of this table into the specified destination.
@brief Returns true if the data in the specified table is identical to the data in this table.
@brief Extends this table by appending rows copied from another table.
@brief Free the internal memory for the specified table.
@brief Get the row at the specified index.
@brief Initialises the table by allocating the internal memory.
@brief Print out the state of this table to the specified stream.
@brief Replace this table’s data by copying from a set of column arrays
@brief Controls the pre-allocation strategy for the ancestral_state column
@brief Controls the pre-allocation strategy for the metadata column
@brief Controls the pre-allocation strategy for this table
@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.
@brief Truncates this table so that only the first num_rows are retained.
@brief Updates the row at the specified index.
@brief Return a description of the specified error.
@brief Builds indexes for this table collection.
@brief Puts the tables into canonical form.
@brief Runs integrity checks on this table collection.
@brief Clears data tables (and optionally provenances and metadata) in this table collection.
@brief Copies the state of this table collection into the specified destination.
@brief Deletes the indexes for this table collection.
@brief Write a table collection to file.
@brief Write a table collection to a stream.
@brief Returns true if the data in the specified table collection is equal to the data in this table collection.
@brief Free the internal memory for the specified table collection.
@brief Returns true if this table collection is indexed.
@brief Sorts the individual table in this collection.
@brief Initialises the table collection by allocating the internal memory and initialising all the constituent tables.
@brief Load a table collection from a file path.
@brief Load a table collection from a stream.
@brief Print out the state of this table collection to the specified stream.
@brief Record the number of rows in each table in the specified tsk_bookmark_t object.
@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.
@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.
@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.
@brief Simplify the tables to remove redundant information.
@brief Sorts the tables in this collection.
@brief Subsets and reorders a table collection according to an array of nodes.
@brief Truncates the tables in this table collection according to the specified bookmark.
@brief Forms the node-wise union of two table collections.
@brief Free the internal memory for the specified table sorter.
@brief Initialises the memory for the sorter object.
@brief Runs the sort using the configured functions.
@brief Set the tree into the null state.
@brief Copies the state of this tree into the specified destination.
@brief Seek to the first tree in the sequence.
@brief Free the internal memory for the specified tree.
@brief Return the length of the branch ancestral to the specified node.
@brief Return number of nodes on the path from the specified node to root.
@brief Returns the leftmost root in this tree.
@brief Compute the most recent common ancestor of two nodes.
@brief Returns the number of roots in this tree.
@brief Counts the number of samples in the subtree rooted at a node.
@brief Returns the parent of the specified node.
@brief Returns the rightmost root in this tree.
@brief Get the list of sites for this tree.
@brief Return an upper bound on the number of nodes reachable from the roots of this tree.
@brief Returns the time of the specified node.
@brief Computes the sum of the lengths of all branches reachable from
the specified node, or from all roots if u=TSK_NULL.
@brief Initialises the tree by allocating internal memory and associating with the specified tree sequence.
@brief Returns true if u is a descendant of v.
@brief Seek to the last tree in the sequence.
@brief Seek to the next tree in the sequence.
@brief Fill an array with the nodes of this tree in postorder.
@brief Fill an array with the nodes of this tree starting from a particular node.
@brief Fill an array with the nodes of this tree in preorder.
@brief Fill an array with the nodes of this tree starting from a particular node.
@brief Seek to the previous tree in the sequence.
@brief Print out the state of this tree to the specified stream.
@brief Seek to a particular position on the genome.
@brief Copies the state of the table collection underlying this tree sequence into the specified destination table collection.
@brief Write a tree sequence to file.
@brief Write a tree sequence to a stream.
@brief Free the internal memory for the specified tree sequence.
@brief Get the breakpoints
@brief Get the discrete genome status
@brief Get the discrete time status
@brief Get a edge by its index
@brief Get the file uuid
@brief Get a individual by its index
@brief Get the top-level tree sequence metadata.
@brief Get the length of top-level tree sequence metadata
@brief Get the top-level tree sequence metadata schema.
@brief Get the length of the top-level tree sequence metadata schema.
@brief Get a edge by its index
@brief Get a mutation by its index
@brief Get a node by its index
@brief Get the number of edges
@brief Get the number of individuals
@brief Get the number of migrations
@brief Get the number of mutations
@brief Get the number of nodes
@brief Get the number of populations
@brief Get the number of provenances
@brief Get the number of samples
@brief Get the number of sites
@brief Return the number of trees in this tree sequence.
@brief Get a population by its index
@brief Get a provenance by its index
@brief Get the map of node id to sample index
@brief Get the samples
@brief Get the sequence length
@brief Get a site by its index
@brief Get the time units string
@brief Get the length of time units string @rst Returns the length of the time units string. @endrst
@brief Initialises the tree sequence based on the specified table collection.
@brief Check if a node is a sample
@brief Load a tree sequence from a file path.
@brief Load a tree sequence from a stream.
@brief Print out the state of this tree sequence to the specified stream.
@brief Create a simplified instance of this tree sequence
@brief Decode the genotypes at the given site, storing them in this variant.
@brief Free the internal memory for the specified variant.
@brief Initialises the variant by allocating the internal memory
@brief Print out the state of this variant to the specified stream.
@brief Copies the state of this variant to another variant
Type Definitions
@brief Container for bitwise flags.
@brief Tskit sizes.
@brief Low-level table sorting method.