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// Copyright (c) 2020 Robert Vaser
#include "bioparser/paf_parser.hpp"
#include <numeric>
#include <string>
#include "biosoup/overlap.hpp"
#include "gtest/gtest.h"
#include "bioparser_test_config.h"
namespace bioparser {
namespace test {
struct PafOverlap: public biosoup::Overlap {
public:
PafOverlap(
const char* q_name, std::uint32_t q_name_len,
std::uint32_t q_len,
std::uint32_t q_begin,
std::uint32_t q_end,
char orientation,
const char* t_name, std::uint32_t t_name_len,
std::uint32_t t_len,
std::uint32_t t_begin,
std::uint32_t t_end,
std::uint32_t score,
std::uint32_t overlap_len,
std::uint32_t quality)
: biosoup::Overlap(
0, q_begin, q_end,
0, t_begin, t_end,
score,
orientation == '+'),
q_name(q_name, q_name_len),
q_len(q_len),
t_name(t_name, t_name_len),
t_len(t_len),
overlap_len(overlap_len),
quality(quality) {}
std::string q_name;
std::uint32_t q_len;
std::string t_name;
std::uint32_t t_len;
std::uint32_t overlap_len;
std::uint32_t quality;
};
class BioparserPafTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
p = Parser<PafOverlap>::Create<PafParser>(BIOPARSER_TEST_DATA + file);
}
void Check() {
EXPECT_EQ(500, o.size());
EXPECT_EQ(96478, std::accumulate(o.begin(), o.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<PafOverlap>& it) {
return s + it->q_name.size() + it->t_name.size();
}));
EXPECT_EQ(18472506, std::accumulate(o.begin(), o.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<PafOverlap>& it) {
return s +
it->lhs_id + it->lhs_begin + it->lhs_end + it->q_len +
it->rhs_id + it->rhs_begin + it->rhs_end + it->t_len +
it->score +
it->strand +
it->overlap_len +
it->quality;
}));
}
std::unique_ptr<Parser<PafOverlap>> p;
std::vector<std::unique_ptr<PafOverlap>> o;
};
TEST_F(BioparserPafTest, ParseWhole) {
Setup("sample.paf");
o = p->Parse(-1);
Check();
}
TEST_F(BioparserPafTest, ParseInChunks) {
Setup("sample.paf");
for (auto t = p->Parse(1024); !t.empty(); t = p->Parse(1024)) {
o.insert(
o.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserPafTest, FormatError) {
Setup("sample.mhap");
try {
o = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::PafParser] error: invalid file format");
}
}
TEST_F(BioparserPafTest, CompressedParseWhole) {
Setup("sample.paf.gz");
o = p->Parse(-1);
Check();
}
TEST_F(BioparserPafTest, CompressedParseInChunks) {
Setup("sample.paf.gz");
for (auto t = p->Parse(1024); !t.empty(); t = p->Parse(1024)) {
o.insert(
o.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserPafTest, CompressedFormatError) {
Setup("sample.mhap.gz");
try {
o = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::PafParser] error: invalid file format");
}
}
} // namespace test
} // namespace bioparser
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