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.


The installation will create you between a test executable (called buildTables) and a library that could be used in any of your programs.

Note: the library usage is simplified since version 1.0.0. If necessary, you can see the details for using previous versions.

Installation from the source code

  1. Unpack the archive
  2. Enter the directory libGkArrays-version-number
  3. Type ./configure
  4. If everything went fine, run make
  5. To install the library on your machine, type make install as an administrator
  6. Afterwards, you may want to run ldconfig as an administrator.
You can specify parameters to the 'configure' script. For instance you can choose to build a static version (quicker) of the library rather than a shared version. Typing ./configure --help will provide you the list of available options.

Installation from the deb package

You just need to install the package using a dedicated program on your distribution or by typing dpkg -i package-name. This will install all the four versions of the library (32 and 64 bits, fixed and variable).

Using Gk-arrays in your code

Inside the archive, you will find under the doc directory a documentation on how to use the Gk-arrays in your code with a simple example.
A full documentation of the library is available online or as a downloadable PDF.

For more information about the Gk-arrays project or download latest update of Gk-arrays, see Gk-arrays project website