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#include <string>
#include <gtest/gtest.h>
#include <alignment/query/PbiFilterZmwGroupQuery.h>
#include <pbdata/testdata.h>
using namespace PacBio;
using namespace PacBio::BAM;
static const std::string testChunking = xmlFile1;
static const std::string testNoFilter = xmlFile2;
static void TestPbiFilterZmwGroupQuery(const std::string& fn, const std::vector<size_t>& expected,
const int32_t min_zmw, const int32_t max_zmw)
{
EXPECT_NO_THROW({
PbiFilterZmwGroupQuery qQuery(fn);
std::vector<size_t> counts;
for (const std::vector<BamRecord>& records : qQuery) {
counts.push_back(records.size());
EXPECT_GT(records.size(), 0u);
std::string movieName = records[0].MovieName();
int32_t holeNumber = records[0].HoleNumber();
EXPECT_TRUE(holeNumber >= min_zmw);
EXPECT_TRUE(holeNumber <= max_zmw);
for (const BamRecord& record : records) {
EXPECT_EQ(holeNumber, record.HoleNumber());
EXPECT_EQ(movieName, record.MovieName());
}
}
EXPECT_EQ(expected, counts);
});
}
static void TestNoneConstPbiFilterZmwGroupQuery(const std::string& fn,
const std::vector<size_t>& expected,
const int32_t min_zmw, const int32_t max_zmw)
{
EXPECT_NO_THROW({
PbiFilterZmwGroupQuery qQuery(fn);
std::vector<size_t> counts;
for (std::vector<BamRecord>& records : qQuery) {
counts.push_back(records.size());
EXPECT_GT(records.size(), 0u);
std::string movieName = records[0].MovieName();
int32_t holeNumber = records[0].HoleNumber();
EXPECT_TRUE(holeNumber >= min_zmw);
EXPECT_TRUE(holeNumber <= max_zmw);
for (BamRecord& record : records) {
EXPECT_EQ(holeNumber, record.HoleNumber());
EXPECT_EQ(movieName, record.MovieName());
}
}
EXPECT_EQ(expected, counts);
});
}
TEST(PbiFilterZmwGroupQueryTest, GetNext)
{
std::string fn = testChunking;
std::vector<size_t> expected({2, 21, 13, 1, 5, 13, 1, 34, 12, 2, 20, 5, 3, 7, 11});
const int32_t min_zmw = 55;
const int32_t max_zmw = 1816;
TestPbiFilterZmwGroupQuery(fn, expected, min_zmw, max_zmw);
TestNoneConstPbiFilterZmwGroupQuery(fn, expected, min_zmw, max_zmw);
}
TEST(PbiFilterZmwGroupQueryTest, NoFilter)
{
std::string fn = testNoFilter;
std::vector<size_t> expected(
{2, 21, 13, 1, 5, 13, 1, 34, 12, 2, 20, 5, 3, 7, 11, 14, 6, 8, 23, 53, 17, 21, 7,
5, 35, 3, 26, 6, 21, 37, 26, 59, 2, 6, 30, 34, 32, 2, 14, 3, 24, 1, 15, 1, 12, 26,
6, 3, 1, 9, 3, 21, 12, 10, 24, 3, 6, 1, 6, 17, 34, 11, 24, 4, 11, 1, 10, 8, 10,
20, 3, 4, 6, 27, 5, 2, 21, 3, 14, 1, 9, 5, 30, 37, 6, 1, 26, 7, 7, 32});
const int32_t min_zmw = 0;
const int32_t max_zmw = 1000000;
TestPbiFilterZmwGroupQuery(fn, expected, min_zmw, max_zmw);
TestNoneConstPbiFilterZmwGroupQuery(fn, expected, min_zmw, max_zmw);
}
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