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/*
* =====================================================================================
*
* Filename: FASTQSequence_gtest.cpp
*
* Description: Test pbdata/FASTQSequence.hpp
*
* Version: 1.0
* Created: 1/13/2017 05:19:13 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <climits>
#include <fstream>
#include <iostream>
#include <gtest/gtest.h>
#include <pbdata/FASTQSequence.hpp>
class FASTQSequenceTest : public ::testing::Test
{
public:
virtual void SetUp() {}
virtual void TearDown() { fastqOne.Free(); }
FASTQSequence fastqOne;
std::streambuf* sbuf;
std::ofstream ofs;
};
TEST_F(FASTQSequenceTest, ReverseComplementSelf)
{
EXPECT_TRUE(fastqOne.title == NULL);
EXPECT_TRUE(fastqOne.titleLength == 0);
EXPECT_TRUE(fastqOne.seq == NULL);
EXPECT_TRUE(fastqOne.length == 0);
EXPECT_FALSE(fastqOne.deleteOnExit);
EXPECT_TRUE(fastqOne.qual.Empty());
EXPECT_TRUE(fastqOne.deletionQV.Empty());
EXPECT_TRUE(fastqOne.insertionQV.Empty());
EXPECT_TRUE(fastqOne.substitutionQV.Empty());
EXPECT_TRUE(fastqOne.mergeQV.Empty());
EXPECT_TRUE(fastqOne.preBaseDeletionQV.Empty());
EXPECT_EQ(fastqOne.GetStorageSize(), 0);
const std::string name = "fastq_seq_one comments";
const std::string s = "TTAGCTAG";
const std::string q = "23!abcde";
const std::string r = "CTAGCTAA";
const std::string rq = "edcba!32";
fastqOne.CopyTitle(name);
EXPECT_EQ(fastqOne.title, name);
static_cast<FASTASequence*>(&fastqOne)->Copy(s);
EXPECT_EQ(fastqOne.length, s.size());
fastqOne.qual.Copy(q);
EXPECT_EQ(fastqOne.qual.ToString(), q);
// Test ReverseComplementSelf()
fastqOne.ReverseComplementSelf();
EXPECT_EQ(memcmp(fastqOne.seq, r.c_str(), r.size() * sizeof(char)), 0);
EXPECT_EQ(fastqOne.title, name);
EXPECT_EQ(fastqOne.qual.ToString(), rq);
}
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