file_mng.h

/*
 * Copyright 2019, José-Manuel Herruzo <jmherruzo@uma.es>,
 *                 Jesús Alastruey-Benedé <jalastru@unizar.es>,
 *                 Pablo Ibáñez-Marín <imarin@unizar.es>
 *
 * This file is part of the bvSFM sequence alignment package.
 *
 * bvSFM is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * bvSFM is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with bvSFM. If not, see <http://www.gnu.org/licenses/>.
 *
 * If you publish any work that uses this software, please cite the following paper:
 *
 * J.M. Herruzo, S. González-Navarro, P. Ibáñez, V. Viñals, J. Alastruey-Benedé, and Óscar Plata.
 * Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor.
 * IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB 2019).
 * DOI: 10.1109/TCBB.2018.2884701 
 * 
 * @article{herruzo2019TCBB,
 *  author    = {José Manuel Herruzo, Sonia González-Navarro, Pablo Ibáñez, Víctor Viñals, Jesús Alastruey-Benedé, and Óscar Plata},
 *  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB 2019)},
 *  title     = {Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor},
 *  year      = {2019},
 *  doi       = {10.1109/TCBB.2018.2884701}
 * }
 *
 */

#ifndef _FILE_MNG_H_
#define _FILE_MNG_H_

#include <stdio.h>
#include "types.h"

/**
  @param file Char array containing the filename
  @param data Char array which will contain all the contents of the array.
  It will be alocated inside the function
  @return 0 if no error occurred.
*/
int file_to_char(const char * file, char ** data);

/**
  @param fp Pointer to the file stream
  @param line String where the data will be saved.
  @return Size of the read sequence
*/
long int read_seq_from_fasta(FILE * fp, char** line);


#endif