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/**
* Copyright INRIA , contributors Peterlongo
* pierre.peterlongo@inria.fr
*
*
* This software is a computer program whose purpose is to detect the
* presence of a sequence in a set of NGS reads, and to compute its average quality and coverage
*
* 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.
*/
/*
* fragment_index.h
*
* Created on: 15 sept. 2010
* Author: ppeterlo
*/
#ifndef FRAGMENT_INDEX_H_
#define FRAGMENT_INDEX_H_
#include <fragment_info.h>
#include <hash.h>
#include <couple.h>
__attribute__((__common__)) int number_of_starters;
__attribute__((__common__)) hash_t seeds; // hash table seed -> (fragment id, position)
__attribute__((__common__)) hash_t seeds_count;
__attribute__((__common__)) couple * seed_table;
p_fragment_info * index_starters_from_input_file (const int k, int nb_events_per_set, const int nb_fragment_per_event, const char input_only_upper, const int index_stride); // read and store all starters presents in the pointed file. Index by seeds of length k all these starters.
void free_seeds_index ();
#endif /* FRAGMENT_INDEX_H_ */
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