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CorrelationMatrixCreatorApplication.hpp
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Thu, May 2, 18:00

CorrelationMatrixCreatorApplication.hpp
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#ifndef CORRELATIONMATRIXCREATORAPPLICATION_HPP
#define CORRELATIONMATRIXCREATORAPPLICATION_HPP
#include <ApplicationInterface.hpp>
#include <MatrixCreator.hpp> // MatrixCreator::methods
#include <string>
/*!
* \brief The CorrelationMatrixCreatorApplication class is a wrapper around a
* RegionMatrixCreator instance creating an autonomous application to
* compute a count matrix from a BAM file by directly passing all the options
* and parameters from the command line.
*/
class CorrelationMatrixCreatorApplication: public ApplicationInterface
{
public:
CorrelationMatrixCreatorApplication() = delete ;
CorrelationMatrixCreatorApplication(const CorrelationMatrixCreatorApplication& app) = delete ;
/*!
* \brief Constructs an object from the command line
* options.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
*/
CorrelationMatrixCreatorApplication(int argn, char** argv) ;
/*!
* \brief Runs the application. The data are classified
* using the given settings and the posterior probability
* matrix is returned through the stdout.
* The matrix is a 4D matrix with dimensions :
* regions, class, shift flip.
* \return an exit code EXIT_SUCCESS or EXIT_FAILURE
* to return to the OS.
*/
virtual int run() override ;
private:
/*!
* \brief Parses the program command line options and
* sets the object field accordingly.
* If the help option is detected, the "runnable"
* field is set to false and subsequent calls to
* run() will produce nothing.
* \param argn the number of options passed to the
* main() function.
* \param argv the vector of options passed to the
* main() function.
* \throw std::invalid_argument if an error is found
* in the program options.
*/
void parseOptions(int argn, char** argv) ;
/*!
* \brief the path to the bed file.
*/
std::string file_bed ;
/*!
* \brief the path to the bam file.
*/
std::string file_bam ;
/*!
* \brief the path to the bam index file.
*/
std::string file_bai ;
/*!
* \brief a relative coordinate indicating the
* most downstream position to consider around
* each region in the bed file.
*/
int from ;
/*!
* \brief a relative coordinate indicating the
* most upstream position to consider around
* each region in the bed file.
*/
int to ;
/*!
* \brief the size of the bin that will be used
* to bin the signal in the regions [from,to] around
* each region in the bed file.
*/
int bin_size ;
/*!
* \brief How to consider the sequenced fragments when computing
* the bin values.
*/
MatrixCreator::methods method ;
/*!
* \brief a flag indicating whether the core of run() can be
* run or not.
*/
bool runnable ;
} ;
#endif // CORRELATIONMATRIXCREATORAPPLICATION_HPP

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