====== Help: LHiSA in C++ ======

The LHiSA project in <nowiki>C++</nowiki> is dedicated to users who want to use LHiSA frequently since the implementation (determination of local high-scoring segments and Monte-Carlo simulations) has been optimized to speed its use. It works along with the Templatized <nowiki>C++</nowiki> Command Line Parser Library ([[http://tclap.sourceforge.net/|TCLAP]] - included in the distribution) and the GNU Scientific Library ([[http://www.gnu.org/software/gsl/|GSL]] - required). The executable can be used to perform LHiSA on genetic data or merely to detect local scores in a sequence.


**(i)**  Requirements:

    * automake/autoconf
    * a <nowiki>C/C++</nowiki> compiler
    * the GNU Scientific Library


**(ii)**  Installation:

    * decompress the archive: **tar zxvf lhisa-x.x.tar.gz**
    * compile the package: **./configure**  then  **make**
    * install the program: **make install**


**(iii)** Performing** LHiSA**:

    * executable: **lhisa**

    * input data file (required): **lhisa -i <filename>**  or  **lhisa < <filename>**  or  **cat <filename> | lhisa**    
The input data file must be in the trinary genetic data format. Refer [[:logiciels:lhisa:trinary_gen_data|here]] for further details on this format or download the {{:logiciels:lhisa:toto.tri|example}}.
    * output data file (required): **lhisa -o <filename>**  or  **lhisa > <filename>** 

    * number of Monte-Carlo simulations (optional): **lhisa -n <number>**    It has an impact on the precision of the p-values. The default value (if not set) is 2000 simulations.
    * threshold or marker level (optional): **lhisa -t <value>**    Threshold upon which we consider that a marker should contribute positively to the score of segment. This level has an impact on the sensibility and specificity of the method. The default value (if not set) is 10%.


**(iv)**  Detecting local scores segments (loss):

    * executable: **lhisa -l**  or  **lhisa --loss**
    * input data file (required):** lhisa -i <filename>**  or  **lhisa < <filename>**  or  **cat <filename> | lhisa**    The input data file is merely a file with the values (in column) of the sequence to submit. Dowload the {{:logiciels:lhisa:toto.seq|example}}.
    * output data file (required): **lhisa -o <filename>**  or  **lhisa > <filename>**

**
(v)**  Other options:

    * help: **lhisa -h**
    * version: **lhisa -v**


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