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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/>
*/
#ifdef CONFIG_HAVE_LIBBZ2
#include "FastqBz2Loader.h"
#include "BzReader.h"
#include <stdlib.h>
#include <fstream>
using namespace std;
FastqBz2Loader::FastqBz2Loader() {
addExtension(".fq.bz2");
addExtension(".fastq.bz2");
}
int FastqBz2Loader::getSize(){
return m_size;
}
int FastqBz2Loader::open(string file){
return openWithPeriod(file,4);
}
int FastqBz2Loader::openWithPeriod(string file,int period){
m_reader.open(file.c_str());
char buffer[RAY_MAXIMUM_READ_LENGTH];
m_loaded=0;
m_size=0;
int rotatingVariable=0;
while(NULL!=m_reader.readLine(buffer,RAY_MAXIMUM_READ_LENGTH)){
if(rotatingVariable==1){
m_size++;
}
rotatingVariable++;
if(rotatingVariable==period){
rotatingVariable=0;
}
}
m_reader.close();
m_reader.open(file.c_str());
return EXIT_SUCCESS;
}
void FastqBz2Loader::load(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator){
loadWithPeriod(maxToLoad,reads,seqMyAllocator,4);
}
// a very simple and compact fastq.gz reader
void FastqBz2Loader::loadWithPeriod(int maxToLoad,ArrayOfReads*reads,MyAllocator*seqMyAllocator,int period){
char buffer[RAY_MAXIMUM_READ_LENGTH];
int rotatingVariable=0;
int loadedSequences=0;
while(loadedSequences<maxToLoad&&NULL!=m_reader.readLine(buffer,RAY_MAXIMUM_READ_LENGTH)){
if(rotatingVariable==1){
Read t;
t.constructor(buffer,seqMyAllocator,true);
reads->push_back(&t);
}
rotatingVariable++;
// a period is reached for each sequence.
if(rotatingVariable==period){
rotatingVariable=0;
m_loaded++;
loadedSequences++;
}
}
if(m_loaded==m_size){
m_reader.close();
}
}
void FastqBz2Loader::close(){
}
#endif
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