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// Copyright (c) 2020 Robert Vaser
#include "bioparser/fastq_parser.hpp"
#include <numeric>
#include "biosoup/sequence.hpp"
#include "gtest/gtest.h"
#include "bioparser_test_config.h"
namespace bioparser {
namespace test {
class BioparserFastqTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
p = Parser<biosoup::Sequence>::Create<FastqParser>(BIOPARSER_TEST_DATA + file);
}
void Check() {
EXPECT_EQ(13, s.size());
EXPECT_EQ(17, std::accumulate(s.begin(), s.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<biosoup::Sequence>& it) {
return s + it->name.size();
}));
EXPECT_EQ(108140, std::accumulate(s.begin(), s.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<biosoup::Sequence>& it) {
return s + it->data.size();
}));
EXPECT_EQ(108140, std::accumulate(s.begin(), s.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<biosoup::Sequence>& it) {
return s + it->quality.size();
}));
}
std::unique_ptr<Parser<biosoup::Sequence>> p;
std::vector<std::unique_ptr<biosoup::Sequence>> s;
};
TEST_F(BioparserFastqTest, ParseWhole) {
Setup("sample.fastq");
s = p->Parse(-1);
Check();
}
TEST_F(BioparserFastqTest, ParseInChunks) {
Setup("sample.fastq");
for (auto t = p->Parse(65536); !t.empty(); t = p->Parse(65536)) {
s.insert(
s.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserFastqTest, FormatError) {
Setup("sample.fasta");
try {
s = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::FastqParser] error: invalid file format");
}
}
TEST_F(BioparserFastqTest, CompressedParseWhole) {
Setup("sample.fastq.gz");
s = p->Parse(-1);
Check();
}
TEST_F(BioparserFastqTest, CompressedParseInChunks) {
Setup("sample.fastq.gz");
for (auto t = p->Parse(65536); !t.empty(); t = p->Parse(65536)) {
s.insert(
s.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserFastqTest, CompressedFormatError) {
Setup("sample.fasta.gz");
try {
s = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::FastqParser] error: invalid file format");
}
}
} // namespace test
} // namespace bioparser
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