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/* ***************************************************************************
*
* KisSplice
* de-novo calling alternative splicing events from RNA-seq data.
*
* ***************************************************************************
*
* Copyright INRIA
* contributors : Vincent Lacroix
* Pierre Peterlongo
* Gustavo Sacomoto
* Vincent Miele
* Alice Julien-Laferriere
* David Parsons
*
* pierre.peterlongo@inria.fr
* vincent.lacroix@univ-lyon1.fr
*
* This software is a computer program whose purpose is to detect alternative
* splicing events from RNA-seq data.
*
* This software is governed by the CeCILL license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL license and that you accept its terms.
*/
#include <stdio.h>
#include "CGraph.h"
#include "BubbleEnumeration.h"
// Functor that print the bc on file
class Printer
{
private:
FILE * _out_file;
public:
Printer(FILE * out_file)
: _out_file(out_file) {}
void operator()(FILE* in_file, int written_lines){
char* buffer = new char[100 * MAX];
for (int i = 0; i < written_lines ; i++) {
fgets(buffer, 100 * MAX, in_file);
fputs(buffer, _out_file);
}
delete[] buffer;
}
};
int main( int argc, char** argv )
{
if ( argc < 8 ){
fprintf( stderr, "Usage: %s infofile contents_file_edges contents_file_nodes basename_edges basename_nodes number_to_read output_file_edges output_file_nodes \n", argv[0] );
exit( EXIT_FAILURE );
}
FILE *output_file_edge = fopen(argv[7], "w");
//if (output_file_edge == NULL) { fprintf(stderr, "Problem opening %s!\n", argv[7]); exit(0); }
FILE *output_file_node = fopen(argv[8], "w");
//if (output_file_node == NULL) { fprintf(stderr, "Problem opening %s!\n", argv[8]); exit(0); }
int required_sequence = atoi( argv[6] );
Printer edgeprinter(output_file_edge);
Printer nodeprinter(output_file_node);
read_edges_and_nodes_withoptimIO<Printer,Printer>
(argv[1],argv[2],argv[3],argv[4],argv[5],&required_sequence, edgeprinter, nodeprinter);
fclose(output_file_edge);
fclose(output_file_node);
}
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