Crate tskit[−][src]
Expand description
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
wrapstsk_table_collection_t
.TreeSequence
wrapstsk_treeseq_t
.Tree
wrapstsk_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.
Prelude
The prelude
module contains definitions that are difficult/annoying to live without.
In particuar, this module exports various traits that make it so that client code does
not have to use
them a la carte.
We recomment that client code import all symbols from this module:
use tskit::prelude::*;
The various documentation examples manually use
each trait both in order
to illustrate which traits are needed and to serve as doc tests.
Optional features
Some features are optional, and are activated by requesting them in your Cargo.toml
file.
provenance
- Enables
provenance
- Enables
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 | Support for table row metadata |
prelude | Export commonly-use types and traits |
provenance | Optional module for table and tree sequence provenance tables. |
types | “Other” tskit types live here. |
Macros
handle_metadata_return | Convenience macro to handle implementing
|
Structs
Enums
NodeTraversalOrder | Specify the traversal order used by
|
Constants
TSK_NULL | “Null” identifier value. |
Traits
NodeListGenerator | Interface for returning lists of node ids from
types implementing |
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. |