superintervals 0.2.0__tar.gz

superintervals-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) [2024] [Kez Cleal]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

superintervals-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: superintervals
+Version: 0.2.0
+Summary: Rapid interval intersections
+Author: Kez Cleal
+Author-email: Kez Cleal <clealk@cardiff.ac.uk>
+License-File: LICENSE
+Requires-Dist: Cython

superintervals-0.2.0/README.md

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+SuperIntervals
+==============
+
+A fast, memory-efficient data structure for interval intersection queries.
+SuperIntervals uses a novel superset-index approach that maintains 
+intervals in position-sorted order, enabling cache-friendly searches and SIMD-optimized counting.
+
+### Features:
+
+- Linear-time index construction from sorted intervals
+- Cache-friendly querying
+- SIMD acceleration (AVX2/Neon) for counting operations
+- Minimal memory overhead (one size_t per interval)
+- Available for C++, Rust, Python, and C
+- Optional Eytzinger memory layout for slightly faster queries (C++/Rust only)
+- No dependencies, header only
+
+
+## Quick Start
+
+- Intervals are considered end-inclusive 
+- The index() function must be called before any queries
+- Found intervals are returned in reverse position-sorted order
+
+### 🐍 Python
+
+```python
+from superintervals import IntervalSet
+
+iset = IntervalSet()
+iset.add(10, 20, 'A')
+iset.index()
+overlaps = iset.find_overlaps(8, 20)
+```
+
+### ⚙️ C++
+```cpp
+#include "SuperIntervals.hpp"
+
+SuperIntervals<int, std::string> intervals;
+intervals.add(1, 5, "A");
+intervals.index();
+std::vector<std::string> results;
+intervals.findOverlaps(4, 9, results);
+```
+
+### 🦀 Rust
+
+```rust
+use super_intervals::SuperIntervals;
+
+let mut intervals = SuperIntervals::new();
+intervals.add(1, 5, "A");
+intervals.index();
+let mut results = Vec::new();
+intervals.find_overlaps(4, 11, &mut results);
+```
+
+
+## Test programs
+Test programs expect plain text BED files and only assess chr1 records - other chromosomes are ignored.
+
+C++ program compares SuperIntervals, ImplicitIntervalTree, IntervalTree and NCLS:
+```
+cd test; make
+./run-cpp-libs a.bed b.bed
+```
+
+Rust program:
+```
+RUSTFLAGS="-Ctarget-cpu=native" cargo run --release --example bed-intersect-si
+cargo run --release --example bed-intersect-si a.bed b.bed
+```
+
+## Benchmark
+
+SuperIntervals (SI) was compared with:
+- Coitrees (Rust: https://github.com/dcjones/coitrees)
+- Implicit Interval Tree (C++: https://github.com/lh3/cgranges)
+- Interval Tree (C++: https://github.com/ekg/intervaltree)
+- Nested Containment List (C: https://github.com/pyranges/ncls/tree/master/ncls/src)
+
+Main results:
+- Roughly ~2-3x faster than the next best library (Coitrees for Rust, Implicit Interval Tree for C++)
+
+### Datasets:
+1. Random regions generated using bedtools
+2. RNA-seq reads and annotations from cgranges repository
+3. ONT reads from sample PAO33946 (chr1, chrM)
+4. Paired-end reads from sample DB53, NCBI BioProject PRJNA417592, (chr1, chrM)
+5. UCSC genes from hg19
+
+Test programs use internal timers and print data to stdout, measuring the 
+index time, and time to find all intersections. Other steps such as file IO are ignored. Test programs also 
+only assess chr1 bed records - other chromosomes are ignored. For 'chrM' records,
+the M was replaced with 1 using sed. Data were assessed in position sorted and random order.
+Datasets can be found on the Releases page, and the `test/run_tools.sh` script has instructions
+for how to repeat the benchmark.
+
+Timings were in microseconds using an i9-11900K, 64 GB, 2TB NVMe machine.
+
+
+### 1. Finding interval intersections
+
+- Coitrees-s uses the `SortedQuerent` version of coitrees
+- SI = superintervals. Eytz refers to the eytzinger layout. `-rs` is the Rust implementation.
+
+#### Intervals in sorted order
+
+|                       | Coitrees | Coitrees-s | SI-rs       | SI-rs     | ImplicitITree-C++ | IntervalTree-C++ | NCLS-C   | SI-C++  | SI-Eytz-C++ |
+| --------------------- | -------- | ---------- |-------------|-----------| ----------------- | ---------------- | -------- |---------|-------------|
+| DB53 reads, ONT reads | 1649.6   | 3169       | 732         | **729**   | 3802.6            | 46393.8          | 10833.6  | 1391.6  | **1365.6**  |
+| DB53 reads, genes     | 54.2     | 82.8       | **21**      | **21**    | 121.6             | 108              | 292.8    | 43      | **40.2**    |
+| ONT reads, DB53 reads | 6487.2   | 3437.2     | 534.6       | **533.6** | 18067.4           | 12448            | 31466.2  | 5333.2  | **4545.2**  |
+| anno, rna             | 49.6     | 33.6       | 17.2        | **17**    | 127.2             | 91.2             | 210.6    | 31.2    | **21.2**    |
+| genes, DB53 reads     | 1171     | 992.8      | 270         | **269.2** | 3141              | 1339.8           | 1768     | 441.8   | **315**     |
+| mito-b, mito-a        | 35046.2  | 35134      | **13115.2** | 13117.2   | 95137.4           | 108567.8         | 250671.8 | 33703.8 | **33298.6** |
+| rna, anno             | 31.8     | 22.6       | **4**       | **4**     | 71.2              | 54               | 238.8    | 29.4    | **27.2**    |
+
+#### Intervals in random order
+
+|                       | Coitrees | Coitrees-s | SI-rs     | SI-Eytz-rs | ImplicitITree-C++ | IntervalTree-C++ | NCLS-C   | SI-C++     | SI-Eytz-C++ |
+| --------------------- | -------- | ---------- |-----------|------------| ----------------- | ---------------- | -------- |------------|-------------|
+| DB53 reads, ONT reads | 2939.6   | 4746.6     | 1323      | **1273**   | 6654.6            | 46771.8          | 12082.4  | 2544.4     | **2180.2**  |
+| DB53 reads, genes     | 75.2     | 131        | 26.6      | **26**     | 168.2             | 122.8            | 308.2    | 56.4       | **51.4**    |
+| ONT reads, DB53 reads | 17100.6  | 19309.2    | 3815      | **3714.6** | 40490.8           | 28633.2          | 55317.6  | 24047      | **23664**   |
+| anno, rna             | 89.6     | 110        | 42.2      | **41.8**   | 188.8             | 150.2            | 299.4    | **58**     | **58**      |
+| genes, DB53 reads     | 2217.6   | 2448.8     | 1343.8    | **1331.6** | 4495.8            | 2747.2           | 3632.2   | **1265.2** | 1730.8      |
+| mito-b, mito-a        | 39002.8  | 88901.8    | **13540** | 13541.8    | 128507.2          | 120712           | 261409.2 | 43682      | **42576.8** |
+| rna, anno             | 51       | 69.2       | 12        | **11.8**   | 140.4             | 84.4             | 323.8    | 54.2       | **53**      |
+
+### 2. Counting interval intersections
+
+#### Intervals in sorted order
+
+|                       | Coitrees | SI-rs     | SI-Eytz-rs | SI-C++    | SI-Eytz-C++ |
+| --------------------- | -------- |-----------|------------|-----------|-------------|
+| DB53 reads, ONT reads | 551.4    | 337.6     | 338        | **239.4** | 265         |
+| DB53 reads, genes     | 26       | 10.6      | 10.8       | 8         | **7**       |
+| ONT reads, DB53 reads | 2517.2   | **795.4** | 796.6      | 2234.2    | 1414.2      |
+| anno, rna             | 26.8     | 13.4      | 13.2       | 22.6      | **12**      |
+| genes, DB53 reads     | 737.4    | **292.6** | 294.6      | 459.6     | 338.2       |
+| mito-b, mito-a        | 7030     | 6634.6    | 6633.4     | 3065.6    | **2991.8**  |
+| rna, anno             | 9        | **4**     | **4**      | 12        | 10          |
+
+#### Intervals in random order
+
+|                       | Coitrees | SI-rs  | SI-Eytz-rs | SI-C++ | SI-Eytz-C++ |
+| --------------------- | -------- | ------ | ---------- | ------ | ----------- |
+| DB53 reads, ONT reads | 1990     | 937.2  | 883.4      | 1018.8 | **789.6**       |
+| DB53 reads, genes     | 49.2     | 16     | 15         | 15.2   | **13.4**        |
+| ONT reads, DB53 reads | 6835     | 4037.8 | **3964.4**     | 8547.8 | 10153.8     |
+| anno, rna             | 52       | 39     | **38.6**       | 47     | 46          |
+| genes, DB53 reads     | 1523.6   | 1261   | 1269       | **1119.4** | 1519.6      |
+| mito-b, mito-a        | 15001.2  | 7290.6 | 7298.4     | 4493.6 | **4452.4**      |
+| rna, anno             | 22       | **12**     | **12**         | 25.2   | 25.4        |
+
+## Python
+
+Install using `pip install .`
+
+```
+from superintervals import IntervalSet
+
+iset = IntervalSet()
+
+# Add interval start, end, identifier. Integer values are supported
+iset.add(10, 20, 0)
+iset.add(19, 18, 1)
+iset.add(8, 11, 2)
+
+# Index method must be called before queries
+iset.index()
+
+iset.any_overlaps(8, 20)
+# >>> True
+
+iset.count_overlaps(8, 20)
+# >>> 3
+
+iset.find_overlaps(8, 20)
+# >>> [1, 0, 2]
+
+iset.set_search_interval(8, 20)
+for itv in iset:
+    print(itv)
+
+# >>> (19, 18, 1) 
+# >>> (10, 20, 0) 
+# >>> (8, 11, 2)
+
+```
+
+## Cpp
+
+```cpp
+#include <iostream>
+#include <vector>
+#include "SuperIntervals.hpp"
+
+int main() {
+    // Create a SuperIntervals instance for integer intervals with string data
+    // Specify with S, T template types
+    SuperIntervals<int, std::string> intervals;
+
+    // Add some intervals
+    intervals.add(1, 5, "Interval A");
+    intervals.add(3, 7, "Interval B");
+    intervals.add(6, 10, "Interval C");
+    intervals.add(8, 12, "Interval D");
+
+    // Index the intervals (must be called before querying)
+    intervals.index();
+
+    // Find overlaps for the range [4, 9]
+    std::vector<std::string> overlaps;
+    intervals.findOverlaps(4, 9, overlaps);
+
+    // Print the overlapping intervals
+    for (const auto& interval : overlaps) {
+        std::cout << interval << std::endl;
+    }
+    
+    // Count the intervals instead
+    std::cout << "Count: " << intervals.countOverlaps(4, 9) << std::endl;
+    
+    // Count stabbed intervals at point 7
+    std::cout << "Number of intervals containing point 7: " << intervals.countStabbed(7) << std::endl;
+
+    return 0;
+}
+```
+There is also a `SuperIntervalsEytz` subclasses that can be used. `SuperIntervalsEytz` 
+uses an Eytzinger memory layout that can sometimes offer faster query times at the cost of higher memory
+usage and slower indexing time.
+
+## Rust
+
+```
+use super_intervals::SuperIntervals;
+
+fn main() {
+    // Create a new instance of SuperIntervals
+    let mut intervals = SuperIntervals::new();
+
+    // Add some intervals with associated data of type T
+    intervals.add(1, 5, "Interval A");
+    intervals.add(10, 15, "Interval B");
+    intervals.add(7, 12, "Interval C");
+
+    // Call index() to prepare the intervals for queries
+    intervals.index();
+
+    // Query for overlapping intervals with a range (4, 11)
+    let mut found_intervals = Vec::new();
+    intervals.find_overlaps(4, 11, &mut found_intervals);
+    
+    // Display found intervals
+    for interval in found_intervals {
+        println!("Found overlapping interval: {}", interval);
+    }
+
+    // Count overlaps with a range (4, 11)
+    let overlap_count = intervals.count_overlaps(4, 11);
+    println!("Number of overlapping intervals: {}", overlap_count);
+}
+```
+There is also `SuperIntervalsEytz` implementation. `SuperIntervalsEytz` 
+uses an Eytzinger memory layout that can sometimes offer faster query times at the cost of higher memory
+usage and slower indexing time.
+
+## Acknowledgements
+
+- The rust test program borrows heavily from the coitrees package
+- The superset-index implemented here exploits a similar interval ordering as described in
+Schmidt 2009 "Interval Stabbing Problems in Small Integer Ranges". However, the superset-index has several advantages including
+  1. An implicit memory layout
+  1. General purpose implementation (not just small integer ranges)
+  1. SIMD counting algorithm 

superintervals-0.2.0/pyproject.toml

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+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "Cython"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "superintervals"
+version = "0.2.0"
+description = "Rapid interval intersections"
+dependencies = ['Cython']
+authors = [{name = "Kez Cleal", email = "clealk@cardiff.ac.uk"}]

superintervals-0.2.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

superintervals-0.2.0/setup.py

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+from setuptools import setup, find_packages, Extension
+from Cython.Build import cythonize
+
+ext_modules = [
+    Extension("superintervals.intervalset",
+              ["src/superintervals/intervalset.pyx"],
+              include_dirs=["src"],
+              language="c++",
+              extra_compile_args=["-std=c++17", "-march=native"])
+]
+
+print('PAKCAGES', find_packages(where='src'))  # Add this line for debugging
+
+setup(
+    name='superintervals',
+    description="Rapid interval intersections",
+    author="Kez Cleal",
+    author_email="clealk@cardiff.ac.uk",
+    packages=find_packages(where='src'),
+    package_dir={"": "src"},
+    install_requires=['Cython'],
+    ext_modules=cythonize(ext_modules),
+)

superintervals-0.2.0/src/superintervals/__init__.py

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+from .intervalset import (
+    IntervalSet
+)