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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/>
*/
#include "FastaLoader.h"
#include <fstream>
#include <stdlib.h>
using namespace std;
/** load sequences */
int FastaLoader::load(string file,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
string id;
ostringstream sequence;
string buffer;
ifstream f(file.c_str());
while(!f.eof()){
buffer="";
f>>buffer;
if(buffer=="")
continue;
if(buffer[0]=='>'){
char bufferForLine[1024];
f.getline(bufferForLine,1024);
if(id!=""){
string sequenceStr=sequence.str();
Read t;
t.constructor(sequenceStr.c_str(),seqMyAllocator,true);
reads->push_back(&t);
}
id=buffer;
sequence.str("");
}else{
sequence<< buffer;
}
}
string sequenceStr=sequence.str();
ostringstream quality;
for(int i=0;i<(int)sequenceStr.length();i++){
quality<< "F";
}
Read t;
t.constructor(sequenceStr.c_str(),seqMyAllocator,true);
reads->push_back(&t);
f.close();
return EXIT_SUCCESS;
}
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