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+ | ====== 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** | ||
+ | |||
+ | |||
+ | Return to the [[:logiciels:lhisa|LHiSA]] main page | ||