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/*
* ============================================================================
*
* Filename: HDFCCSReader_gtest.cpp
*
* Description: Test hdf/HDFCCSReader.hpp
*
* Version: 1.0
* Created: 08/23/2013 10:17:14 AM
* Revision: 08/20/2014
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* ============================================================================
*/
#include <gtest/gtest.h>
#include <pbdata/testdata.h>
#include <hdf/HDFCCSReader.hpp>
#include <pbdata/CCSSequence.hpp>
using namespace H5;
class HDFCCSReaderTEST : public ::testing::Test
{
public:
virtual void SetUp() {}
virtual void TearDown() {}
};
TEST_F(HDFCCSReaderTEST, ReadCCSFromBasH5)
{
std::string fileName = baxFile2;
HDFCCSReader<CCSSequence> reader;
reader.InitializeDefaultIncludedFields();
ASSERT_EQ(reader.Initialize(fileName), 1);
ASSERT_EQ(reader.GetMovieName(),
"m130220_114643_42129_c100471902550000001823071906131347_s1_p0");
CCSSequence seq;
for (int i = 0; i < 1000; i++) {
reader.GetNext(seq);
}
reader.Close();
}
TEST_F(HDFCCSReaderTEST, ReadCCSFromCCSH5)
{
std::string fileName = ccsFile1;
HDFCCSReader<CCSSequence> reader;
reader.SetReadBasesFromCCS();
reader.InitializeDefaultIncludedFields();
ASSERT_EQ(reader.Initialize(fileName), 1);
ASSERT_EQ(reader.GetMovieName(),
"m130328_211423_ethan_c100499512550000001823070408081371_s1_p0");
CCSSequence seq;
for (int i = 0; i < 1000; i++) {
reader.GetNext(seq);
}
reader.Close();
}
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