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genogrove\n\n[![Ubuntu](https://img.shields.io/github/actions/workflow/status/genogrove/genogrove/ci-ubuntu.yml?branch=main\u0026label=Ubuntu\u0026style=flat)](https://github.com/genogrove/genogrove/actions/workflows/ci-ubuntu.yml)\n[![macOS](https://img.shields.io/github/actions/workflow/status/genogrove/genogrove/ci-macos.yml?branch=main\u0026label=macOS\u0026style=flat)](https://github.com/genogrove/genogrove/actions/workflows/ci-macos.yml)\n![Compilers](https://img.shields.io/badge/compilers-GCC%2013--14%20|%20Clang%2016--18%20|%20Apple%20Clang-informational)\n[![Release](https://img.shields.io/github/v/release/genogrove/genogrove)](https://github.com/genogrove/genogrove/releases/latest)\n![C++20](https://img.shields.io/badge/C%2B%2B-20-blue.svg)\n[![Downloads](https://img.shields.io/github/downloads/genogrove/genogrove/total.svg)](https://github.com/genogrove/genogrove/releases)\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)\n[![GitHub stars](https://img.shields.io/github/stars/genogrove/genogrove)](https://github.com/genogrove/genogrove/stargazers)\n[![GitHub issues](https://img.shields.io/github/issues/genogrove/genogrove)](https://github.com/genogrove/genogrove/issues)\n![CodeRabbit Pull Request Reviews](https://img.shields.io/coderabbit/prs/github/genogrove/genogrove?utm_source=oss\u0026utm_medium=github\u0026utm_campaign=genogrove%2Fgenogrove\u0026labelColor=171717\u0026color=FF570A\u0026link=https%3A%2F%2Fcoderabbit.ai\u0026label=CodeRabbit+Reviews)\n\nA 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.\n\n## Quick Start\n\n```bash\ngit clone https://github.com/genogrove/genogrove.git\ncd genogrove\ncmake -S . -B build -DCMAKE_BUILD_TYPE=Release\ncmake --build build\n```\n\nFor testing, add `-DBUILD_TESTING=ON`. For the CLI, add `-DBUILD_CLI=ON`.\n\n## Example\n\n```cpp\n#include \u003cgenogrove/structure/grove/grove.hpp\u003e\n#include \u003cgenogrove/io/bed_reader.hpp\u003e\n\nnamespace ggs = genogrove::structure;\nnamespace gio = genogrove::io;\nnamespace gdt = genogrove::data_type;\n\n// Load intervals from a BED file\nggs::grove\u003cgdt::interval, gio::bed_entry\u003e grove;\ngio::bed_reader reader(\"regions.bed\");\nfor (const auto\u0026 entry : reader) {\n    grove.insert_data(entry.chrom, gdt::interval(entry.start, entry.end - 1), entry);\n}\n\n// Query overlapping intervals\ngdt::interval query(1000, 2000);\nauto results = grove.intersect(query, \"chr1\");\nfor (auto* key : results.get_keys()) {\n    auto\u0026 data = key-\u003eget_data();\n    // data.chrom, data.start, data.end, data.name, ...\n}\n```\n\n## Language Bindings\n\n- [pygenogrove](https://github.com/genogrove/pygenogrove) (python)\n- [genogrove-r](https://github.com/genogrove/genogrove-r) (R)\n- [genogrove-rs](https://github.com/genogrove/genogrove-rs) (Rust)\n\n## Compiler Support\n\n| Platform | Compiler | Versions |\n|----------|----------|----------|\n| Ubuntu 24.04 | GCC | 13, 14 |\n| Ubuntu 24.04 | Clang (LLVM) | 16, 17, 18 |\n| macOS 14 | Apple Clang | 15 (Xcode 15.4) |\n| macOS 15 | Apple Clang | 16 (Xcode 16.x) |\n\nAll configurations are tested in both Debug and Release modes.\n\n## Documentation\n\nFull documentation is available at [www.genogrove.com](https://www.genogrove.com).\n\n## License\n\n[GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenogrove%2Fgenogrove","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenogrove%2Fgenogrove","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenogrove%2Fgenogrove/lists"}