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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2010, 2011, 2012, 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/>
*/
#include "FastqLoader.h"
#include <code/Mock/constants.h>
#include <fstream>
#include <stdlib.h>
using namespace std;
FastqLoader::FastqLoader() {
addExtension(".fastq");
addExtension(".fq");
m_f = NULL;
}
int FastqLoader::open(string file){
return openWithPeriod(file,4);
}
int FastqLoader::openWithPeriod(string file,int period){
m_f=fopen(file.c_str(),"r");
//cout << "[DEBUG] counting entries" << endl;
m_lineReader.initialize();
m_size=0;
m_loaded=0;
int rotatingVariable=0;
char buffer[RAY_MAXIMUM_READ_LENGTH];
while(NULL!= m_lineReader.readLine(buffer,RAY_MAXIMUM_READ_LENGTH,m_f)){
/*
if(m_size > 7000000)
//cout << "[DEBUG] buffer= " << buffer << endl;
*/
if(rotatingVariable==1){
m_size++;
}
rotatingVariable++;
if(rotatingVariable==period){
rotatingVariable=0;
}
/*
if(m_size % 1000 == 0)
//cout << "[DEBUG] m_size= " << m_size << endl;
*/
}
//cout << "[DEBUG] m_size= " << m_size << endl;
fclose(m_f);
m_f=fopen(file.c_str(),"r");
m_lineReader.reset();
return EXIT_SUCCESS;
}
void FastqLoader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
//cout << "[DEBUG] loading fastq file maxToLoad= " << maxToLoad << endl;
loadWithPeriod(maxToLoad,reads,seqMyAllocator,4);
}
void FastqLoader::loadWithPeriod(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator,int period){
char buffer[RAY_MAXIMUM_READ_LENGTH];
int rotatingVariable=0;
int loadedSequences=0;
//cout << "[DEBUG] loadWithPeriod m_loaded= " << m_loaded << " m_size= " << m_size << endl;
while(loadedSequences<maxToLoad && NULL != m_lineReader.readLine(buffer,RAY_MAXIMUM_READ_LENGTH,m_f)){
// pick up the sequence data
if(rotatingVariable == 1){
Read t;
t.constructor(buffer,seqMyAllocator,true);
reads->push_back(&t);
}
rotatingVariable++;
// a period is reached for each read.
if(rotatingVariable==period){
rotatingVariable=0;
loadedSequences++;
m_loaded++;
}
}
if(m_loaded==m_size){
close();
}
}
int FastqLoader::getSize(){
return m_size;
}
void FastqLoader::close(){
if(m_f != NULL) {
fclose(m_f);
m_f = NULL;
}
m_lineReader.destroy();
}
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