O(1) region count queries using sparse prefix sums

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  • License: MIT
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libSps is a versatile C++ library designed for efficiently analyzing n-dimensional data. Specifically, it implements constant-time hyperrectangle count queries using a sparse prefix sum index. libSps is available as a header-only library for C++ as well as a Python 3 module. It is based on algorithms developed by Shekelyan et al. [1] and Schmidt et al. [2].

The library is ideal for processing contact mapping data (https://en.wikipedia.org/wiki/Chromosome_conformation_capture), and is therefore used in Smoother (https://github.com/Siegel-Lab/BioSmoother).

libSps’s documentation is available at https://libsps.readthedocs.io/.

[1] Shekelyan, M., Dignös, A. & Gamper, J. Sparse prefix sums: Constant-time range sum queries over sparse multidimensional data cubes. Information Systems 82, 136–147 (2019).

[2] Schmidt et al. @todo

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