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
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
/*
* =====================================================================================
*
* Filename: FASTQReader_gtest.cpp
*
* Description: Test pbdata/FASTQReader.hpp
*
* Version: 1.0
* Created: 10/29/2012 05:19:32 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <gtest/gtest.h>
#include <pbdata/testdata.h>
#include <pbdata/FASTQReader.hpp>
const std::string movie = "m130328_211423_ethan_c100499512550000001823070408081371_s1_p0";
const int numSeqs = 208;
class FASTQReaderTest : public ::testing::Test
{
public:
void SetUp()
{
std::string filename(fastqFile1);
reader.Initialize(filename);
}
void TearDown()
{
reader.Close();
seq.Free();
}
FASTQReader reader;
FASTQSequence seq;
};
TEST_F(FASTQReaderTest, GetNext)
{
reader.GetNext(seq);
EXPECT_EQ(std::strcmp(seq.title, std::string(movie + "/8").c_str()), 0);
EXPECT_EQ(seq.length, 752u);
std::string expected_seq(
"AATAAAAAAAAAAGAAAGCTTCGAAGTGAGCGAATTACTCTCAGGCAACT"
"GCGGGTGAAGCCAGAGCAGGCATGATGACACTGGGGAATTTACGCAAATT"
"TTACCATTGAATTTACACATGCGATGTGCTGGAATGCGGAAGACGGAAAC"
"GAAACCAGCAATACATCAAACGCCGCACCAGAGAAGAGATATTTGCGCCC"
"TAAACTAGGTAAGGCGGTTGACTTGAACAGCAAATCAAACGTCAACGAGC"
"AGCGTGAGTATATACAAGTTATCTCGGATGGAGAACGTATTCTAAATGTA"
"AGCACGAATCCCGGAAGAGGAAACCAGTTTCTTGGTTTTTCGCCATCCTC"
"GAAGACCTGTTACAAACCGCACTGGACCTGGAAAGTTTCTGCGCGTAATC"
"GACAAGACTAGTAACTATCGACATCAACCATCGATTACGGGTTGGGTCAA"
"TGGGTTCAGATGCAGGTGAGTATCCTTCATATGATAGTCTGACGCTGGCA"
"TTCGCTCAAAGGAAGTAGACGGTTTTGTAAATAGAAACGCTTGTGAAAAG"
"CTGAATTTCGCGTCGTCTTCCAGCGATGCAGAGCTGTAGTAGTTCAGATG"
"ATGACCGTTACTCAAAGTGCCTGCAACGGCTCGGGGCGTGCGCGTCCTGT"
"GGTGGCTGCTTTTGTTGCGCTGTTTGCAGTGTATGGTTGTCGGGTGATGT"
"TGCCTGCAAACCCACAAAACCCCACACACACAACAGTTGGGTTGTTGATT"
"GG");
std::string expected_qual("(,)'(')''++),.$\"+*$'--.-/+&.$-./$',-.&#'/,.,)-,--,");
for (size_t i = 0; i < seq.length; i++) {
EXPECT_EQ(seq.seq[i], expected_seq[i]);
}
for (size_t i = 0; i < expected_qual.size(); i++) {
EXPECT_EQ(seq.qual[i] + FASTQSequence::charToQuality, expected_qual[i]);
}
reader.GetNext(seq);
EXPECT_EQ(strcmp(seq.title, std::string(movie + "/9").c_str()), 0);
// Continue to read
for (int i = 2; i < numSeqs; i++) {
EXPECT_TRUE(reader.GetNext(seq));
}
EXPECT_EQ(std::strcmp(seq.title, std::string(movie + "/249").c_str()), 0);
// Can not proceed.
EXPECT_FALSE(reader.GetNext(seq));
}
|
