Crate range_set_blaze

Expand description

§range-set-blaze

Integer sets as fast, sorted, integer ranges with full set operations

The integers can be any size (u8 to u128) and may be signed (i8 to i128). The set operations include union, intersection, difference, symmetric difference, and complement.

The crate’s main struct is RangeSetBlaze, a set of integers. See the documentation for details.

Unlike the standard BTreeSet and HashSet, RangeSetBlaze does not store every integer in the set. Rather, it stores sorted & disjoint ranges of integers in a cache-efficient BTreeMap. It differs from other interval libraries – that we know of – by offering full set operations and by being optimized for sets of clumpy integers.

We can construct a RangeSetBlaze from unsorted & redundant integers (or ranges). When the inputs are clumpy, construction will be linear in the number of inputs and set operations will be sped up quadratically.

The crate’s main trait is SortedDisjoint. It is implemented by iterators of sorted & disjoint ranges of integers. See the SortedDisjoint documentation for details.

With any SortedDisjoint iterator we can perform set operations in one pass through the ranges and with minimal (constant) memory. It enforces the “sorted & disjoint” constraint at compile time. This trait is inspired by the SortedIterator trait from the sorted_iter crate. SortedDisjoint differs from its inspiration by specializing on disjoint integer ranges.

The crate supports no_std, WASM, and embedded projects. Use the command:

cargo add range-set-blaze --features "alloc" --no-default-features

§Benchmarks

See the benchmarks for performance comparisons with other range-related crates.

Generally, for many tasks involving clumpy integers and ranges, RangeSetBlaze is much faster than alternatives.

The benchmarks are in the benches directory. To run them, use cargo bench.

§Articles

Nine Rules for Creating Fast, Safe, and Compatible Data Structures in Rust: Lessons from RangeSetBlaze in Towards Data Science. It provides a high-level overview of the crate and its design.
Nine Rules for Running Rust on the Web and on Embedded: Practical Lessons from Porting range-set-blaze to no_std and WASM in Towards Data Science. It covers porting to “no_std”.
Check AI-Generated Code Perfectly and Automatically My Experience Applying Kani’s Formal Verification to ChatGPT-Suggested Rust Code. Shows how to prove overflow safety.
Nine Rules to Formally Validate Rust Algorithms with Dafny in Towards Data Science. It shows how to formally validate one of the crate’s algorithms.
Nine Rules for SIMD Acceleration of your Rust Code: General Lessons from Boosting Data Ingestion in the range-set-blaze Crate by 7x in Towards Data Science
Also see: CHANGELOG

§Examples

Example 1

Here we take the union (operator “|”) of two RangeSetBlaze’s:

Example 1

use range_set_blaze::RangeSetBlaze;

 // a is the set of integers from 100 to 499 (inclusive) and 501 to 1000 (inclusive)
let a = RangeSetBlaze::from_iter([100..=499, 501..=999]);
 // b is the set of integers -20 and the range 400 to 599 (inclusive)
let b = RangeSetBlaze::from_iter([-20..=-20, 400..=599]);
// c is the union of a and b, namely -20 and 100 to 999 (inclusive)
let c = a | b;
assert_eq!(c, RangeSetBlaze::from_iter([-20..=-20, 100..=999]));

Example 2

In biology, suppose we want to find the intron regions of a gene but we are given only the transcription region and the exon regions.

Example 2

We create a RangeSetBlaze for the transcription region and a RangeSetBlaze for all the exon regions. Then we take the difference between the transcription region and exon regions to find the intron regions.

use range_set_blaze::RangeSetBlaze;

let line = "chr15   29370   37380   29370,32358,36715   30817,32561,37380";

// split the line on white space
let mut iter = line.split_whitespace();
let chr = iter.next().unwrap();

// Parse the start and end of the transcription region into a RangeSetBlaze
let trans_start: i32 = iter.next().unwrap().parse().unwrap();
let trans_end: i32 = iter.next().unwrap().parse().unwrap();
let trans = RangeSetBlaze::from_iter([trans_start..=trans_end]);
assert_eq!(trans, RangeSetBlaze::from_iter([29370..=37380]));

// Parse the start and end of the exons into a RangeSetBlaze
let exon_starts = iter.next().unwrap().split(',').map(|s| s.parse::<i32>());
let exon_ends = iter.next().unwrap().split(',').map(|s| s.parse::<i32>());
let exon_ranges = exon_starts
    .zip(exon_ends)
    .map(|(s, e)| s.unwrap()..=e.unwrap());
let exons = RangeSetBlaze::from_iter(exon_ranges);
assert_eq!(
    exons,
    RangeSetBlaze::from_iter([29370..=30817, 32358..=32561, 36715..=37380])
);

// Use 'set difference' to find the introns
let intron = trans - exons;
assert_eq!(intron, RangeSetBlaze::from_iter([30818..=32357, 32562..=36714]));
for range in intron.ranges() {
    let (start, end) = range.into_inner();
    println!("{chr}\t{start}\t{end}");
}

Modules§

prelude: This prelude module provides a convenient way to import the most commonly used types, traits, and functions.

Macros§

intersection_dyn: Intersects one or more SortedDisjoint iterators, creating a new SortedDisjoint iterator. The input iterators need not to be of the same type.
union_dyn: Unions one or more SortedDisjoint iterators, creating a new SortedDisjoint iterator. The input iterators need not to be of the same type.

Structs§

AssumeSortedStarts: Gives any iterator of ranges the SortedStarts trait without any checking.
CheckSortedDisjoint: Gives the SortedDisjoint trait to any iterator of ranges. The iterator will panic if/when it finds that the ranges are not actually sorted and disjoint.
DynSortedDisjoint: Gives SortedDisjoint iterators a uniform type. Used by the union_dyn and intersection_dyn macros to give all their input iterators the same type.
IntoIter: A (double-ended) iterator over the integer elements of a RangeSetBlaze.
IntoRangesIter: An iterator that moves out the ranges in the RangeSetBlaze, i.e., the integers as sorted & disjoint ranges.
Iter: A (double-ended) iterator over the integer elements of a RangeSetBlaze.
KMerge: Works with UnionIter to turn two SortedDisjoint iterators into a SortedDisjoint iterator of their union, i.e., all the integers in any input iterator, as sorted & disjoint ranges.
Merge: Works with UnionIter to turn any number of SortedDisjoint iterators into a SortedDisjoint iterator of their union, i.e., all the integers in any input iterator, as sorted & disjoint ranges.
NotIter: Turns a SortedDisjoint iterator into a SortedDisjoint iterator of its complement, i.e., all the integers not in the original iterator, as sorted & disjoint ranges.
RangeSetBlaze: A set of integers stored as sorted & disjoint ranges.
RangesIter: An iterator that visits the ranges in the RangeSetBlaze, i.e., the integers as sorted & disjoint ranges.
RogsIterDeprecated: Experimental: An iterator over Rogs (ranges or gaps) in a RangeSetBlaze.
UnionIter: Turns any number of SortedStarts iterators into a SortedDisjoint iterator of their union, i.e., all the integers in any input iterator, as sorted & disjoint ranges. Uses Merge or KMerge.

Enums§

RogDeprecated: Experimental: Represents an range or gap in a RangeSetBlaze.

Traits§

Integer: The element trait of the RangeSetBlaze and SortedDisjoint, specifically u8 to u128 (including usize) and i8 to i128 (including isize).
MultiwayRangeSetBlaze: The trait used to provide methods on multiple RangeSetBlaze’s, specifically union and intersection.
MultiwayRangeSetBlazeRef: The trait used to provide methods on multiple RangeSetBlaze references, specifically union and intersection.
MultiwaySortedDisjoint: The trait used to define methods on multiple SortedDisjoint iterators, specifically union and intersection.
SortedDisjoint: The trait used to mark iterators that provide ranges that are sorted by start and disjoint. Set operations on iterators that implement this trait can be performed in linear time.
SortedStarts: A trait used to mark iterators that provide ranges sorted by start, but not necessarily by end, and may overlap.

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