//Copyright inria / irisa (2013)
//
//
//raluca.uricaru@gmail.com
//pierre.peterlongo@inria.fr
//
//This software is a computer program whose purpose is to call SNPs from NGS reads.
//
//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.

/*
 * commons.h
 *
 *  Created on: 17 sept. 2010
 *      Author: ppeterlo
 */

#ifndef COMMONS_H_
#define COMMONS_H_
#include<stdio.h>
#include<string.h>

//using namespace std;

#include "../minia/Kmer.h" // FOR uint64_t and kmer_type

void revcomp(char *s, int len);
void rev(char s[], int len);
void init_static_variables();
char * to_upper (char  * word);
char * to_lower (char  * word);
char ** sort_strings (char ** strings, int number);
uint64_t codeSeed_uint64_t(const char *seq);
int valid_character(const char c);
void print_rev_comp(char s[], FILE * out=stdout);
// macro to test if a variable is null (i.e., a malloc failed)
#define test_alloc( variable) {	if(variable == NULL){		fprintf(stderr,"cannot allocate memory for variable %s, exit\n",#variable);		exit(1);	}}
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
#define Sinc24(a)  ((a == 0xFFFFFF ) ? 0xFFFFFF : a++)
#define Sinc8(a)  ((a == 0xFF ) ? 0xFF : a++)
#endif /* COMMONS_H_ */
