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//
// fastqdataset.cpp
// Mothur
//
// Created by Sarah Westcott on 3/31/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#include "fastqdataset.h"
/***********************************************************************/
TestFastqDataSet::TestFastqDataSet() { m = MothurOut::getInstance(); }
/***********************************************************************/
vector<string> TestFastqDataSet::getSubsetFRFastq(int numSeqs) {
fillForwardFastq();
fillReverseFastq();
ofstream out, out2;
util.openOutputFile("tempForward.txt", out); util.openOutputFile("tempReverse.txt", out2);
for (int i = 0; i < numSeqs; i++) {
ffastqReads[i].printFastq(out);
rfastqReads[i].printFastq(out2);
}
vector<string> filenames; filenames.push_back("tempForward.txt"); filenames.push_back("tempReverse.txt");
return filenames;
}
/***********************************************************************/
void TestFastqDataSet::fillForwardFastq() {
ffastqReads.clear();
//read info from stable file
string testfile = "/Users/sarahwestcott/Desktop/mothur/TestMothur/TestFiles/F8D0_S345_L001_R1_001.fastq";
ifstream in;
util.openInputFile(testfile, in);
int count = 0; bool ignore = false; string format = "illumina1.8+";
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
if (count < 2000) {
FastqRead read(in, ignore, format); util.gobble(in);
if (!ignore) { ffastqReads.push_back(read); count++; }
}else { break; }
}
in.close();
}
/***********************************************************************/
void TestFastqDataSet::fillReverseFastq() {
rfastqReads.clear();
//read info from stable file
string testfile = "/Users/sarahwestcott/Desktop/mothur/TestMothur/TestFiles/F8D0_S345_L001_R2_001.fastq";
ifstream in;
util.openInputFile(testfile, in);
int count = 0; bool ignore = false; string format = "illumina1.8+";
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
if (count < 2000) {
FastqRead read(in, ignore, format); util.gobble(in);
if (!ignore) { rfastqReads.push_back(read); count++; }
}else { break; }
}
in.close();
}
/***********************************************************************/
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