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.

Installation

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

You can have a 32-bit and 64-bit library as well as a fixed and a variable-length read library. Hence depending on the options you specify, you may have between one and four versions of the library.

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
You can specify parameters to the 'configure' script. By default, make will create a 32-bit implementation of the Gk-arrays for variable-length reads. If you have lots of reads, then you need the 64-bit implementation. If your reads all have the same length, then you should use the fixed-length read implementation which runs much faster. For both cases, there exists an option in the configure script: If you specify both options, you will end with four versions of the library:

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.