1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
#include <string>
#include <gtest/gtest.h>
#include <alignment/query/SequentialZmwGroupQuery.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 TestSequentialZmwGroupQuery(const std::string& fn, const std::vector<int>& expected)
{
EXPECT_NO_THROW({
std::vector<int> counts;
SequentialZmwGroupQuery qQuery(fn);
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();
for (const BamRecord& record : records) {
EXPECT_EQ(holeNumber, record.HoleNumber());
EXPECT_EQ(movieName, record.MovieName());
}
}
EXPECT_EQ(expected, counts);
});
}
static void TestNoneConstSequentialZmwGroupQuery(const std::string& fn,
const std::vector<int>& expected)
{
EXPECT_NO_THROW({
std::vector<int> counts;
SequentialZmwGroupQuery qQuery(fn);
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();
for (BamRecord& record : records) {
EXPECT_EQ(holeNumber, record.HoleNumber());
EXPECT_EQ(movieName, record.MovieName());
}
}
EXPECT_EQ(expected, counts);
});
}
TEST(SequentialZmwGroupQueryTest, CountQSizes)
{
std::string fn = bamFile1;
std::vector<int> expected({2, 2, 10, 2, 3, 1, 2, 2, 3, 4, 1, 3, 1, 1, 2, 2,
2, 2, 1, 1, 1, 2, 2, 2, 3, 8, 1, 3, 2, 1, 15, 2,
1, 3, 1, 2, 2, 1, 3, 3, 2, 2, 1, 2, 2, 1, 1, 1});
TestSequentialZmwGroupQuery(fn, expected);
TestNoneConstSequentialZmwGroupQuery(fn, expected);
}
TEST(SequentialZmwGroupQueryTest, Chunking)
{
std::string fn = testChunking;
std::vector<int> 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});
TestSequentialZmwGroupQuery(fn, expected);
}
|
