Code and benchmarks for paper "Practical Variable Length Gap Pattern Matching" (SEA 2016, http://link.springer.com/chapter/10.1007/978-3-319-38851-9_1). Based on https://github.com/simongog/sdsl-lite
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README.md

SDSL - Succinct Data Structure Library

Build Status

What is it?

The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic lower bound of the object while supporting operations of the original object efficiently. The theoretical time complexity of an operation performed on the classical data structure and the equivalent succinct data structure are (most of the time) identical.

Why SDSL?

Succinct data structures have very attractive theoretical properties. However, in practice implementing succinct data structures is non-trivial as they are often composed of complex operations on bitvectors. The SDSL Library provides high quality, open source implementations of many succinct data structures proposed in literature.

Specifically, the aim of the library is to provide basic and complex succinct data structure which are

  • Easy and intuitive to use (like the STL, which provides classical data structures),
  • Faithful to the original theoretical results,
  • Capable of handling large inputs (yes, we support 64-bit),
  • Provide efficient construction of all implemented succinct data structures, while at the same time enable good run-time performance.

In addition we provide additional functionality which can help you use succinct data structure to their full potential.

  • Each data structure can easily be serialized and loaded to/from disk.
  • We provide functionality which helps you analyze the storage requirements of any SDSL based data structure (see right)
  • We support features such as hugepages and tracking the memory usage of each SDSL data structure.
  • Complex structures can be configured by template parameters and therefore easily be composed. There exists one simple method which constructs all complex structures.
  • We maintain an extensive collection of examples which help you use the different features provided by the library.
  • All data structures are tested for correctness using a unit-testing framework.
  • We provide a large collection of supporting documentation consisting of examples, cheat sheet, tutorial slides and walk-through.

The library contains many succinct data structures from the following categories:

  • Bitvectors supporting Rank and Select
  • Integer Vectors
  • Wavelet Trees
  • Compressed Suffix Arrays (CSA)
  • Balanced Parentheses Representations
  • Longest Common Prefix (LCP) Arrays
  • Compressed Suffix Trees (CST)
  • Range Minimum/Maximum Query (RMQ) Structures

For a complete overview including theoretical bounds see the cheat sheet or the wiki.

Documentation

We provide an extensive set of documentation describing all data structures and features provided by the library. Specifically we provide

  • A cheat sheet which succinctly describes the usage of the library.
  • An doxygen generated API reference which lists all types and functions of the library.
  • A set of example programs demonstrating how different features of the library are used.
  • A tutorial presentation with the example code using in the sides demonstrating all features of the library in a step-by-step walk-through.
  • Unit Tests which contain small code snippets used to test each library feature.

Requirements

The SDSL library requires:

  • A modern, C++11 ready compiler such as g++ version 4.9 or higher or clang version 3.2 or higher.
  • The cmake build system.
  • A 64-bit operating system. Either Mac OS X or Linux are currently supported.
  • For increased performance the processor of the system should support fast bit operations available in SSE4.2

Installation

To download and install the library use the following commands.

git clone https://github.com/simongog/sdsl-lite.git
cd sdsl-lite
./install.sh

This installs the sdsl library into the include and lib directories in your home directory. A different location prefix can be specified as a parameter of the install.sh script:

./install /usr/local/

To remove the library from your system use the provided uninstall script:

./uninstall.sh

Getting Started

To get you started with the library you can start by compiling the following sample program which constructs a compressed suffix array (a FM-Index) over the text mississippi!, counts the number of occurrences of pattern si and stores the data structure, and a space usage visualization to the files fm_index-file.sdsl and fm_index-file.sdsl.html:

#include <sdsl/suffix_arrays.hpp>
#include <fstream>

using namespace sdsl;

int main() {
    csa_wt<> fm_index;
    construct_im(fm_index, "mississippi!", 1);
    std::cout << "'si' occurs " << count(fm_index,"si") << " times.\n";
    store_to_file(fm_index,"fm_index-file.sdsl");
    std::ofstream out("fm_index-file.sdsl.html");
    write_structure<HTML_FORMAT>(fm_index,out);
}

To compile the program using g++ run:

g++ -std=c++11 -O3 -DNDEBUG -I ~/include -L ~/lib program.cpp -o program -lsdsl -ldivsufsort -ldivsufsort64

Next we suggest you look at the comprehensive tutorial which describes all major features of the library or look at some of the provided examples.

Test

Implementing succinct data structures can be tricky. To ensure that all data structures behave as expected, we created a large collection of unit tests which can be used to check the correctness of the library on your computer. The test directory contains test code. We use googletest framework and make to run the tests. See the README file in the directory for details.

To simply run all unit tests after installing the library type

cd sdsl-lite/build
make test-sdsl

Note: Running the tests requires several sample files to be downloaded from the web and can take up to 2 hours on slow machines.

Benchmarks

To ensure the library runs efficiently on your system we suggest you run our benchmark suite. The benchmark suite recreates a popular experimental study which you can directly compare to the results of your benchmark run.

Bug Reporting

While we use an extensive set of unit tests and test coverage tools you might still find bugs in the library. We encourage you to report any problems with the library via the github issue tracking system of the project.

The Latest Version

The latest version can be found on the SDSL github project page https://github.com/simongog/sdsl-lite .

If you are running experiments in an academic settings we suggest you use the most recent released version of the library. This allows others to reproduce your experiments exactly.

Licensing

The SDSL library is free software provided under the GNU General Public License (GPLv3). For more information see the COPYING file in the library directory.

We distribute this library freely to foster the use and development of advanced data structure. If you use the library in an academic setting please cite the following paper:

@inproceedings{gbmp2014sea,
  title     = {From Theory to Practice: Plug and Play with Succinct Data Structures},
  author    = {Gog, Simon and Beller, Timo and Moffat, Alistair and Petri, Matthias},
  booktitle = {13th International Symposium on Experimental Algorithms, (SEA 2014)},
  year      = {2014},
  pages     = {326-337},
  ee        = {http://dx.doi.org/10.1007/978-3-319-07959-2_28}
}

A preliminary version if available here on arxiv.

External Resources used in SDSL

We have included the code of two excellent suffix array construction algorithms.

Additionally, we use the googletest framework to provide unit tests. Our visualizations are implemented using the d3js-library.

Authors

The main contributors to the library are:

This project is also supported by code contributions from other researchers. E.g. Juha Kärkkäinen, Dominik Kempa, and Simon Puglisi contributed a compressed bitvector implementation (hyb_vector). This project further profited from excellent input of our students Markus Brenner, Alexander Diehm, Christian Ocker, and Maike Zwerger. Stefan Arnold helped us with tricky template questions. We are also grateful to Diego Caro, Travis Gagie, Kalle Karhu, Bruce Kuo, Jan Kurrus, Shanika Kuruppu, Jouni Siren, and Julio Vizcaino for bug reports.

Contribute

Are you working on a new or improved implementation of a succinct data structure? We encourage you to contribute your implementation to the SDSL library to make your work accessible to the community within the existing library framework. Feel free to contact any of the authors or create an issue on the issue tracking system.