Expand description
‘chaintools’ is a library for serializing and working with genomic chain files in Rust.
This crate provides two main entries:
ReaderandWriterfor reading and writing encoded chain files.ChainMapand inner structs for performing basic operations (filter, sort, etc) on chain files.
§Reading chain files
The entrypoint for reading genomic chain files in the ‘chaintools’ Rust library is through
the Reader struct, offering methods like [Reader::from_file] to create a reader from a file path
and return a Result with a [ChainMap], [Reader::from_bytes] to create a reader from a byte slice,
[Reader::from_bin] to create a reader from a binary file path, and [Reader::load_chain] to load a
specific chain from a binary file using a chain ID. Internally, the Reader struct handles file
operations, parsing byte data efficiently, and utilizes Rust’s standard library for file I/O
and parallel processing for parsing and filtering chain data, providing a comprehensive interface
for working with genomic chain files in various formats within Rust.
§Examples
use chaintools::cmap::ChainMap;
use chaintools::Reader;
let reader: ChainMap = Reader::from_file("path/to/chainfile.chain")?;§Operations over chain files
The ChainMap struct provides a variety of methods for performing operations on chain files,
including filtering, sorting, inserting, removing, and iterating over chains, making it very
flexible to work with. Operations like [ChainMap::filter] and [ChainMap::iter] allow users
to filter and iterate over chains in a chain file, while [ChainMap::get] and [ChainMap::insert]
allow users to get and insert chains into a chain file. The ChainMap struct also provides specific
filtering methods like [ChainMap::filter_id] and [ChainMap::filter_score] to filter chains by ID
and score, respectively. This set of methods is inteded to grow over time as more operations are
needed for working with genomic chain files in Rust (e.g., merging, splitting, etc).
On top of these operations, the Chain struct provides a simple interface for working with individual chains, allowing users to access chain data like ID, score, and blocks, as well as perform basic string operations mainly, such as accessing chain information or converting chain data to a string. A Chain is composed by two inner structs, ChainHead and AlignmentRecord, which represent the chain header and alignment block, respectively, and provide methods for accessing and manipulating chain data. The basic picture of the choosen way to represent a .chain file in this crate is basically a json-like structure, where each chain is a set of inner structs, and each inner struct is a set of fields, which can be accessed and manipulated by the user.
§Examples
use chaintools::cmap::ChainMap;
use chaintools::Reader;
use chaintools::cmap::Chain;
let reader: ChainMap = Reader::from_file("path/to/chainfile.chain")?;
let chain: Chain = reader.get(10);§Writing chain files
The Writer struct provides a simple interface for writing genomic chain files in Rust, offering
a discrete set of methods in this release, such as [Writer::to_bin] to write a encoded chain
file and [Writer::to_bin_gz] to write an encoded and gz compressed chain file in cases were
the size of the file is a concern.
§Examples
use chaintools::cmap::ChainMap;
use chaintools::Reader;
use chaintools::Writer;
let chains: ChainMap = Reader::from_file("path/to/chainfile.chain")?;
let filt_chains = chains.filter(|c| c.score > 1000);
Writer::to_bin(&filt_chains, "path/to/chainfile.chain");