Crate tskit

A rust interface to tskit.

This crate provides a mapping of the tskit C API to rust. The result is an interface similar to the tskit Python interface, but with all operations implemented using compiled code.

Features

Interface to the C library

• TableCollection wraps tsk_table_collection_t.
• TreeSequence wraps tsk_treeseq_t.
• Tree wraps tsk_tree_t.
• Tree iteration occurs via traits from streaming_iterator.
• Errors returned from C map to TskitError::ErrorCode. Their string messages can be obtained by printing the error type.

Safety

• The types listed above handle all the memory management!
• All array accesses are range-checked.
• Object lifetimes are clear:
  • Creating a tree sequence moves/consumes a table collection.
  • Tree lifetimes are tied to that of the parent tree sequence.
  • Table objects (NodeTable, etc..) are only represented by non-owning, immutable types.

Optional features

Some features are optional, and are activated by requesting them in your Cargo.toml file.

• provenance
  • Enables provenance

To add features to your Cargo.toml file:

[dependencies]
tskit = {version = "0.2.0", features=["feature0", "feature1"]}

What is missing?

• A lot of wrappers to the C functions.
• Tree sequence statistics!

Re-exports

pub use bindings::TSK_NODE_IS_SAMPLE;
pub use bindings::tsk_flags_t;
pub use bindings::tsk_id_t;
pub use bindings::tsk_size_t;
pub use error::TskitError;

Modules

bindings	Low-level (“unsafe”) bindings to the C API.
error	Error handling
ffi	Define traits related to wrapping tskit stuff
metadata
provenance	Optional module for table and tree sequence provenance tables.
types	“Other” tskit types live here.

Structs

EdgeTable	An immutable view of an edge table.
EdgeTableRow	Row of an EdgeTable
IndividualTable	An immutable view of a individual table.
IndividualTableRow	Row of a IndividualTable
MigrationTable	An immutable view of a migration table.
MigrationTableRow	Row of a MigrationTable
MutationTable	An immutable view of site table.
MutationTableRow	Row of a MutationTable
NodeTable	An immtable view of a node table.
NodeTableRow	Row of a NodeTable
PopulationTable	An immutable view of site table.
PopulationTableRow	Row of a PopulationTable
SimplificationOptions	Control the behavior of crate::TableCollection::simplify and crate::TreeSequence::simplify
SiteTable	An immutable view of site table.
SiteTableRow	Row of a SiteTable
TableClearOptions	Modify behavior of crate::TableCollection::clear.
TableCollection	A table collection.
TableEqualityOptions	Modify behavior of crate::TableCollection::equals.
TableOutputOptions	Modify behavior of crate::TableCollection::dump.
TableSortOptions	Modify behavior of crate::TableCollection::sort.
Tree	A Tree.
TreeFlags	Specify the behavior of iterating over [Tree] objects. See [TreeSequence::tree_iterator].
TreeSequence	A tree sequence.
TreeSequenceFlags	Modify behavior of crate::TableCollection::tree_sequence and crate::TreeSequence::new.

Enums

NodeTraversalOrder

Specify the traversal order used by Tree::traverse_nodes.

Constants

TSK_NULL

“Null” identifier value.

Traits

NodeIterator	Trait defining iteration over nodes.
NodeListGenerator	Interface for returning lists of node ids from types implementing TableAccess.
TableAccess	Immutable access to tables.
TskitTypeAccess	Provide pointer access to underlying C types

Functions

c_api_major_version	C API major version
c_api_minor_version	C API minor version
c_api_patch_version	C API patch version
c_api_version	The C API version in MAJOR.MINOR.PATCH format
version	Version of the rust crate.

Type Definitions

TskReturnValue

Handles return codes from low-level tskit functions.