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This web page will no longer be updated. Seethe author's web pagesfor further releases.

RLCSA [4, 3, 7]is a compressed suffix array implementation that has been optimized for highlyrepetitive text collections. Examples of such collections include version control dataand individual genomes. This implementation also serves as a testbed for many techniquesused with compressed suffix arrays.The most up-to-date description of RLCSA can be found in [7].

The current version includes experimental support for:

LCP information [5]
Distribution-aware sampling [6, 9]
Adaptive distribution-aware sampling
Space-efficient document listing [8]

See README in the package for further information.The implementation is available for download under the MIT / X11 License.

There is also a separate package containing implementations of additional document retrieval algorithms:

Brute-force document listing and top-k document retrieval.
New variants of PDL for document listing and top-k document retrieval [10].
Several variants of Sadakane's algorithm for document listing.

Full experimental results from [10] are also included in the document listing package.

News

2014-07-23 This web page will no longer be updated. See the author's web pages for further releases.
2014-04-18 An updated version of the document listing package, with a minor bug fix to RLCSA to support it.
2014-01-11 A new version of the document listing package, and some new datasets from [10].
2014-01-10 A new version with a number of technical changes. Required by January 2014 version of the doclist package.
2013-05-21 A separate package with some additional document listing algorithms.
2013-05-20 A new version with improved document listing support.
2013-04-10 A new version with document listing support.
2013-01-21 A new version with parallel sampling.
2012-12-07 A new version with various changes accumulated over time.
2012-11-05 More test data is now available online.
2012-10-12 More test data is now available online.
2012-02-14 More space-efficient construction. Option to use a succinct bit vector to mark sampled positions.
2011-08-23 A minor update to support the August 2011 version of GCSA.
2011-05-17 Support for distribution-aware sampling and an improved low-level interface for external modules.
2011-01-17 A new version that supports the interface used in recent GCSA experiments.
2010-11-25 Added a list of the data sets used in the experiments.
2010-10-13 A new version with libstdc++ parallel mode support and performance improvements.
2010-03-29 A new version with some compatibility and interface updates.
2010-01-11 A new version with experimental support for LCP information.
2009-11-25 A new version of RLCSA is available. This version includes bug fixes, more functionality and a bit cleaner interface.
2009-06-15 The implementation of RLCSA is now available.

Downloads

Current versions

RLCSA (April 2014)
Document listing (April 2014)

RLCSA

April 2014. A minor bug fix version to support the April 2014 version of the document listing package.
January 2014. This version includes a more consistent interface, faster SA construction for small alphabets, and some additions to the library. Required by January 2014 version of the doclist package.
May 2013. This version contains a simplified construction program for a single file as well as improved document listing support. Most importantly, the grammar rules in precomputed document listing are no longer run-length encoded if that increases their size.
April 2013. This version includes preliminary support for document listing using precomputed answers. A modified web graph compressor (Hernández, Navarro; SPIRE 2012) is required for building the document listing structure. The source code for it is available upon request. This version was used for the experiments in [8].
January 2013. This version includes a multi-threaded sampling algorithm for finding (almost) optimal distribution-aware samples quickly. There is also some undocumented work on document listing with highly repetitive data. This version was used in the experiments in [9].
December 2012. This version has many technical changes from the earlier versions. This version is required by the December 2012 version of GCSA.
February 2012. Construction algorithm for partial indexes changed from multiple Larsson-Sadakane algorithms to a parallel prefix-doubling algorithm. Succinct bit vectors can be used instead of gap encoded ones to e.g. mark sampled positions. This version was used in the experiments in [7].
August 2011. Minor updates to some library functions. This version is required by the August 2011 version of GCSA.
May 2011. The low-level interface has been improved in this version. Weighted / distribution-aware sampling is now also supported. The test program has also been extended.
January 2011. This version has a low-level interface compatible with that of GCSA. Also, the default sample rate was changed to more realistic 128, and the test program supports patterns in Pizza&Chili format.
October 2010. This version supports libstdc++ parallel mode as an alternative to MCSTL. There are also some speed optimizations (an alternative encoding for run-length encoded bit vectors and improved display()).
March 2010. Fixed some problems when compiling with a new version of g++. RLCSA now uses iterators and const operations to make parallelization easier.
January 2010. Includes experimental support for LCP information. This version was used in the experiments reported in [5].
November 2009. A cleaned up version with more functionality.
June 2009. This version was used in the experiments reported in [3]. There are some bugs that were introduced when cleaning up the code. You should use the November 2009 version instead.

Document listing

April 2014. A new variant of top-k PDL. Some technical updates and bug fixes. This package was used for the experiments in [10]. The package also includes full experimental results from [10]. Requires April 2014 version of RLCSA.
January 2014. A major update for the experiments in [10]. Requires January 2014 version of RLCSA.
May 2013. This is the initial release of the document listing package. The ILCP implementation is a rewrite of the one used in [8]. The package requires May 2013 version of RLCSA.

Data

The following data sets were used in experiments with RLCSA. Some of them are available fromthe Pizza&Ch

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