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//
// testfastqread.cpp
// Mothur
//
// Created by Sarah Westcott on 3/29/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#include "testfastqread.h"
#include "dataset.h"
/**************************************************************************************************/
TestFastqRead::TestFastqRead() { //setup
m = MothurOut::getInstance();
TestFastqDataSet data;
reads = data.getForwardFastq();
filenames = data.getSubsetFRFastq(100);
}
/**************************************************************************************************/
TestFastqRead::~TestFastqRead() {
for (int i = 0; i < filenames.size(); i++) { util.mothurRemove(filenames[i]); }
//teardown
}
/**************************************************************************************************/
//Using ATGCGTCATC & 40 39 38 37 36 35 34 33 32 31
TEST(Test_Container_FastqRead, FastqReadConstructor) {
TestFastqRead testFastq;
vector<int> scores; for (int i = 31; i < 41; i++) { scores.push_back(i); }
Sequence seq("testSeq", "ATGCGTCATC");
QualityScores qual("testSeq", scores);
FastqRead read(seq, qual);
EXPECT_EQ(read.getSeq(), "ATGCGTCATC");
EXPECT_EQ(read.getScores()[0], 31);
}
TEST(Test_Container_FastqRead, FastqReadFromFileConstructor) {
TestFastqRead testFastq;
ifstream in; bool ignore; string format = "illumina1.8+";
Utils util; util.openInputFile(testFastq.filenames[0], in);
FastqRead read(in, ignore, format);
EXPECT_EQ(read.getSeq(), (testFastq.reads[0]).getSeq());
EXPECT_EQ(read.getScores()[0], testFastq.reads[0].getScores()[0]);
}
/**************************************************************************************************/
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