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An interval tree library interpretation based on augmented AVL balanced binary trees.

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libitree

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About libitree

Libitree is a simple C library for handling interval trees.

Installation

$ ./configure
$ make
$ make check
$ sudo make install

This will install the static library libitree.a in the autotools default location (/usr/local/lib). Support for building a shared library will be added soon.

See INSTALL for more detailed building and installation instructions.

Usage

Proper documentation will be added soon. At the moment, look at the test suite under the tests directory, the interval_tree.c test suite in particular, for examples on how to use the library.

Supported Compilers

The following compilers are known to work:

  • GCC 4.8 - 7.2
  • Clang 3.5 - 5.0

In particular, the following compilers are currently used in continuous integration at Travis:

Compiler Operating System Version String
GCC 4.9.4 Ubuntu 14.04.5 LTS gcc-4.9 (Ubuntu 4.9.4-2ubuntu1~14.04.1) 4.9.4
GCC 5.4.1 Ubuntu 14.04.5 LTS gcc-5 (Ubuntu 5.4.1-2ubuntu1~14.04) 5.4.1
GCC 6.3.0 Ubuntu 14.04.5 LTS gcc-6 (Ubuntu/Linaro 6.3.0-18ubuntu2~14.04) 6.3.0
GCC 7.2.0 Ubuntu 14.04.5 LTS gcc-7 (Ubuntu 7.2.0-1ubuntu1~14.04) 7.2.0
Clang 3.5.0 Ubuntu 14.04.5 LTS clang version 3.5.0-4ubuntu2~trusty2 (tags/RELEASE_350/final)
Clang 3.6.2 Ubuntu 14.04.5 LTS clang version 3.6.2-svn240577-1~exp1 (branches/release_36)
Clang 3.7.1 Ubuntu 14.04.5 LTS clang version 3.7.1-svn253571-1~exp1 (branches/release_37)
Clang 3.8.0 Ubuntu 14.04.5 LTS clang version 3.8.0-2ubuntu3~trusty5 (tags/RELEASE_380/final)
Clang 3.9.1 Ubuntu 14.04.5 LTS clang version 3.9.1-4ubuntu3~14.04.2 (tags/RELEASE_391/rc2)
Clang 4.0.1 Ubuntu 14.04.5 LTS clang version 4.0.1-svn305264-1~exp1 (branches/release_40)
Clang 5.0.0 Ubuntu 14.04.5 LTS clang version 5.0.0-svn310902-1~exp1 (branches/release_500_final)

Known Bugs and Limitations

Interval equality checks are at the moment based on float comparison which is obviously not ideal. As a result, the structure of the tree and the results of search queries might slightly vary across different architectures. I will switch to using a more robust approach when finding a rather stable solution.

License and Copyright

The library is licensed under the MIT License:

Copyright © 2018 Alessandro Vullo

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.

Acknowledgements

I am very grateful to Julienne Walker for generously providing the source code of his production quality C AVL balanced tree library. Libitree has been designed as an expanded adaptation of this library.

Thanks to Niels Lohmann from which I borrowed the skeleton of the travis configuration file from his JSON C++ library.

Projects using libitree

ensembl-xs

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An interval tree library interpretation based on augmented AVL balanced binary trees.

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