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/*
* ==========================================================================
*
* Filename: HDFZMWReader_gtest.cpp
*
* Description: Test hdf/HDFZMWReader.hpp
*
* Version: 1.0
* Created: 08/21/2013 07:00:49 PM
* 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/HDFZMWReader.hpp>
using namespace H5;
class HDFZMWReaderTEST : public ::testing::Test
{
public:
virtual void SetUp() {}
virtual void TearDown() {}
void Initialize(H5File &pbihdfFile, std::string fileName, std::string groupName,
HDFGroup &callsGroup)
{
try {
FileAccPropList propList;
pbihdfFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
} catch (Exception &e) {
std::cout << "ERROR, could not open hdf file" << fileName << ", exiting." << std::endl;
std::exit(EXIT_FAILURE);
}
ASSERT_NE(callsGroup.Initialize(pbihdfFile, groupName), 0);
/*
HDFGroup rootGroup, pulseDataGroup;
if (rootGroup.Initialize(pbihdfFile, "/") == 0) {
std::cout << "ERROR, could not open /" << std::endl;
std::exit(EXIT_FAILURE);
}
if (pulseDataGroup.Initialize(rootGroup, "PulseData") == 0){
std::cout << "ERROR, could not open /PulseData" << std::endl;
std::exit(EXIT_FAILURE);
}
ASSERT_NE(callsGroup.Initialize(pulseDataGroup, "BaseCalls"), 0);
*/
}
void Close(H5File &pbihdfFile, HDFGroup &callsGroup)
{
pbihdfFile.close();
callsGroup.Close();
}
void TestGetNext(HDFZMWReader &zmwReader)
{
UInt count = 0;
ZMWGroupEntry entry;
while (zmwReader.GetNext(entry)) {
count++;
ASSERT_EQ(zmwReader.curZMW, count);
}
ASSERT_EQ(count, zmwReader.nZMWEntries);
}
};
TEST_F(HDFZMWReaderTEST, ReadZMWFromBaseCalls)
{
HDFZMWReader zmwReader;
std::string fileName = baxFile2;
std::string groupName = "/PulseData/BaseCalls";
H5File pbihdfFile;
HDFGroup baseCallsGroup;
Initialize(pbihdfFile, fileName, groupName, baseCallsGroup);
ASSERT_NE(zmwReader.Initialize(&baseCallsGroup), 0);
TestGetNext(zmwReader);
zmwReader.Close();
Close(pbihdfFile, baseCallsGroup);
}
TEST_F(HDFZMWReaderTEST, ReadZMWFromPulseCalls)
{
std::string fileName = plsFile1;
H5File pbihdfFile;
try {
FileAccPropList propList;
pbihdfFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
} catch (Exception &e) {
std::cout << "ERROR, could not open hdf file" << fileName << ", exiting." << std::endl;
std::exit(EXIT_FAILURE);
}
HDFGroup pulseCallsGroup;
ASSERT_NE(pulseCallsGroup.Initialize(pbihdfFile, "/PulseData/PulseCalls"), 0);
HDFZMWReader zmwReader;
ASSERT_NE(zmwReader.Initialize(&pulseCallsGroup), 0);
TestGetNext(zmwReader);
zmwReader.Close();
// Switch to read from CCS ZMW.
HDFGroup ccsGroup;
ASSERT_NE(ccsGroup.Initialize(pbihdfFile, "/PulseData/ConsensusBaseCalls"), 0);
ASSERT_NE(zmwReader.Initialize(&ccsGroup), 0);
TestGetNext(zmwReader);
zmwReader.Close();
// Close
ccsGroup.Close();
pulseCallsGroup.Close();
pbihdfFile.close();
}
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