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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
* Copyright (C) 2013 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 SequenceFileDetectorHeader
#define SequenceFileDetectorHeader
#include <RayPlatform/core/OperatingSystem.h>
/**
*
* This class receives a directory
* and returns the valid genomic files.
*
* \author Sébastien Boisvert
*/
class SequenceFileDetector {
char m_directorySeparator;
vector<string> m_leftFiles;
vector<string> m_rightFiles;
vector<string> m_singleFiles;
void gatherAllFiles(string & root, vector<string> & rawFiles);
string replaceString(const string & templateString, const string & oldString,
const string & newString);
public:
SequenceFileDetector();
/**
* Detect all supported files in a directory, recursively.
*/
void detectSequenceFiles(string & directory);
vector<string> & getLeftFiles();
vector<string> & getRightFiles();
vector<string> & getSingleFiles();
};
#endif
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