Crate handlegraph

A Rusty take on the libhandlegraph interface for variation graph access and manipulation.

Overview

This crate provides a number of traits that together encapsulate the handlegraph interface. While these traits do not form a direct mirror of the C++ interface, (almost) all of the features should exist and be usable.

In addition to the abstract traits, there are currently two concrete handlegraphs that implement them:

• HashGraph is a HashMap-based graph that does nothing to reduce its memory footprint, but is fast.
• PackedGraph uses packed integer vectors to greatly reduce memory usage.

The interface

The handlegraph interface is split into three categories, each consisting of a number of traits that encapsulate a subset of the functionality implied by their category.

• handlegraph is for immutable access to the nodes and edges of a graph
• mutablehandlegraph is for mutable access to nodes and edges
• pathhandlegraph is for both immutable and mutable access to the paths embedded in a graph

Handles and NodeIds

The core types, used all over the various traits, are defined in handle:

• NodeId is a newtype used as a node identifier
• Handle represents a specific orientation of a node
• Edge is a newtype for edges in a specific order

Misc.

• conversion has some functions for converting from GFA to a handlegraph and back
• packed is where the packed vector collection types used by PackedGraph are implemented

Modules

algorithms
consensus
conversion
disjoint	Rust implementation of the lock-free parallel disjoint set described in the paper "Wait-free Parallel Algorithms for the Union-Find Problem" by Richard J. Anderson and Heather Woll.
handle
handlegraph	Traits for immutable access to a HandleGraph, including its nodes/handles, edges, and the sequences of nodes.
hashgraph	A handlegraph implementation using HashMap to represent the graph topology and nodes, and each path as a Vec of nodes.
mutablehandlegraph	Traits for manipulating the nodes and edges of a graph.
packed
packedgraph	A handlegraph implementation using packed vector representations to minimize memory usage.
pathhandlegraph	Traits and utilities for accessing and manipulating paths embedded in a graph.
util

Macros

assign_fields_local
assign_for_fields
impl_one_based_index
impl_one_based_index_default
impl_space_usage
impl_space_usage_stack_newtype