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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program 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, version 3 of the License.
This program 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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _common_functions
#define _common_functions
#include "constants.h"
#ifdef CONFIG_MPI_IO
#include <mpi.h>
#endif
#include <code/KmerAcademyBuilder/Kmer.h>
#include <code/SeedingData/GraphPath.h>
#include <code/SeedingData/PathHandle.h>
#include <RayPlatform/memory/allocator.h>
#include <RayPlatform/core/slave_modes.h>
#include <RayPlatform/core/master_modes.h>
#include <RayPlatform/communication/mpi_tags.h>
#include <string.h>
#include <string>
#include <iostream>
#include <vector>
#ifdef CONFIG_ASSERT
#include <assert.h>
#endif
using namespace std;
/*
* Encode a char
*/
uint8_t charToCode(char a);
/*
* verify that x has only A,T,C, and G
*/
bool isValidDNA(char*x);
/*
* transform a string in a Kmer
*/
Kmer wordId(const char*a);
/*
* add line breaks to a string
*/
string addLineBreaks(string sequence,int a);
/*
* TODO: move this in GraphPath
*/
string convertToString(GraphPath*b,int m_wordSize,bool color);
Kmer kmerAtPosition(const char*string,int pos,int w,char strand,bool color);
PathHandle getPathUniqueId(int rank,int id);
int getIdFromPathUniqueId(PathHandle a);
int getRankFromPathUniqueId(PathHandle a);
void print64(uint64_t a);
void print8(uint8_t a);
char complementNucleotide(char c);
/*
* complement the sequence of a biological thing
*/
string reverseComplement(string*a);
MessageUnit pack_pointer(void**pointer);
void unpack_pointer(void**pointer,MessageUnit integerValue);
bool flushFileOperationBuffer(bool force,ostringstream*buffer,ostream*file,int bufferSize);
bool flushFileOperationBuffer_FILE(bool force,ostringstream*buffer,FILE*file,int bufferSize);
#ifdef CONFIG_MPI_IO
bool flushFileOperationBuffer_MPI_IO(bool force,ostringstream*buffer,MPI_File file,int bufferSize);
#endif
#endif
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