https://github.com/genogrove/genogrove

Modern C++ genome indexing library
https://github.com/genogrove/genogrove

bplustree cpp data-structures genogrove genome genomics graph indexing intervals

Last synced: 21 days ago
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Modern C++ genome indexing library

• Host: GitHub
• URL: https://github.com/genogrove/genogrove
• Owner: genogrove
• License: gpl-3.0
• Created: 2025-10-01T06:10:40.000Z (6 months ago)
• Default Branch: main
• Last Pushed: 2026-01-26T21:45:34.000Z (about 2 months ago)
• Last Synced: 2026-01-27T08:46:33.567Z (about 2 months ago)
• Topics: bplustree, cpp, data-structures, genogrove, genome, genomics, graph, indexing, intervals
• Language: C++
• Homepage: https://genogrove.readthedocs.io
• Size: 99 MB
• Stars: 2
• Watchers: 1
• Forks: 2
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
# genogrove

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A C++20 library for efficient genomic interval storage and querying using a specialized B+ tree data structure (grove). Supports BED, GFF/GTF, and SAM/BAM formats with an optional CLI.

## Quick Start

```bash

git clone https://github.com/genogrove/genogrove.git

cd genogrove

cmake -S . -B build -DCMAKE_BUILD_TYPE=Release

cmake --build build

```

For testing, add `-DBUILD_TESTING=ON`. For the CLI, add `-DBUILD_CLI=ON`.

## Example

```cpp

#include 

#include 

namespace ggs = genogrove::structure;

namespace gio = genogrove::io;

namespace gdt = genogrove::data_type;

// Load intervals from a BED file

ggs::grove grove;

gio::bed_reader reader("regions.bed");

for (const auto& entry : reader) {

    grove.insert_data(entry.chrom, gdt::interval(entry.start, entry.end - 1), entry);

}

// Query overlapping intervals

gdt::interval query(1000, 2000);

auto results = grove.intersect(query, "chr1");

for (auto* key : results.get_keys()) {

    auto& data = key->get_data();

    // data.chrom, data.start, data.end, data.name, ...

}

```

## Language Bindings

- [pygenogrove](https://github.com/genogrove/pygenogrove) (python)

- [genogrove-r](https://github.com/genogrove/genogrove-r) (R)

- [genogrove-rs](https://github.com/genogrove/genogrove-rs) (Rust)

## Compiler Support

| Platform | Compiler | Versions |

|----------|----------|----------|

| Ubuntu 24.04 | GCC | 13, 14 |

| Ubuntu 24.04 | Clang (LLVM) | 16, 17, 18 |

| macOS 14 | Apple Clang | 15 (Xcode 15.4) |

| macOS 15 | Apple Clang | 16 (Xcode 16.x) |

All configurations are tested in both Debug and Release modes.

## Documentation

Full documentation is available at [www.genogrove.com](https://www.genogrove.com).

## License

[GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html)