Crate gbwt 

GBWT: Graph BWT

This is a Rust reimplementation of parts of the GBWT and the GBWTGraph. It is based on the Simple-SDS library.

References

GBWT

Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, and Richard Durbin: Haplotype-aware graph indexes.
Bioinformatics 36(2):400-407, 2020. DOI: 10.1093/bioinformatics/btz575

GBWTGraph

Jouni Sirén, Jean Monlong, Xian Chang, Adam M. Novak, Jordan M. Eizenga, Charles Markello, Jonas A. Sibbesen, Glenn Hickey, Pi-Chuan Chang, Andrew Carroll, Namrata Gupta, Stacey Gabriel, Thomas W. Blackwell, Aakrosh Ratan, Kent D. Taylor, Stephen S. Rich, Jerome I. Rotter, David Haussler, Erik Garrison, and Benedict Paten:
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
Science 374(6574):abg8871, 2021. DOI: 10.1126/science.abg8871

GBZ

Jouni Sirén and Benedict Paten: GBZ file format for pangenome graphs.
Bioinformatics 38(22):5012-5018, 2022. DOI: 10.1093/bioinformatics/btac656

Notes

• See Simple-SDS for assumptions on the environment.
• This implementation supports the Simple-SDS file formats for GBWT and GBZ.
• GBWT / GBZ files written by this library can be identified by source tag value jltsiren/gbwt-rs.

Re-exports

pub use crate::bwt::Pos;

pub use crate::gbwt::GBWT;

pub use crate::gbwt::SearchState;

pub use crate::gbwt::BidirectionalState;

pub use crate::gbwt::Metadata;

pub use crate::gbwt::PathName;

pub use crate::gbwt::FullPathName;

pub use crate::gbz::GBZ;

pub use crate::graph::Segment;

pub use crate::support::GraphPosition;

pub use crate::support::Orientation;

Modules

algorithms

Algorithms using GBWT and GBZ.

bwt

The BWT stored as an array of compressed node records.

gbwt

GBWT: A run-length encoded FM-index storing paths as sequences of node identifiers.

gbz

GBZ: Space-efficient representation for a subset of GFA.

graph

GBWTGraph: Node sequences and node-to-segment translation.

headers

File format headers.

support

Support structures for GBWT and GBZ.

Constants

ENDMARKER

Node identifier 0 is used for technical purposes and does not exist in the graph.

REFERENCE_SAMPLES_KEY

Key for the tag listing the names of reference samples.

REF_SAMPLE

Sample name for generic named paths.

SOURCE_KEY

Key of the source tag.

SOURCE_VALUE

Value of the source tag.