ATGC: Gk-Arrays

Gk-arrays: Querying large read collections in main memory: a versatile data structure.

Philippe N., Salson M., Lecroq T., Leonard M., Commes T., Rivals E.

Please cite THIS paper if you use Gk-arrays.

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Gk-arrays source code is distributed under the GPL-compliant CeCILL-C license.

Source code

Version 1.0.0: libGkArrays-1.0.0.tar.gz
Version 0.2.0: libGkArrays-0.2.0.tar.gz

Debian/Ubuntu package

Version 1.0.0 (64 bit architecture): libGkArrays_1.0.0_amd64.deb
Version 1.0.0 (32 bit architecture): libGkArrays_1.0.0_i386.deb
Version 0.2.0 (64 bit architecture): libGkArrays_0.2.0_amd64.deb
Version 0.2.0 (32 bit architecture): libGkArrays_0.2.0_i386.deb

A very simple test file can be downloaded from here.
Once the library is installed, you can compile it using e.g. g++ -Wall -pedantic -O3 -lGkArrays testGkArrays.cpp -o testGkArrays.
Another test file (measuring the query time) is also included in the source code under the src directory.