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
|
#include "gtest/gtest.h"
#include "Variant.h"
#include <iostream>
#include <string>
#include <vector>
TEST(VariantCallFile, open){
vcflib::VariantCallFile variantFile;
std::string filename = "../samples/sample.vcf";
variantFile.open(filename);
ASSERT_TRUE(variantFile.is_open());
};
TEST(VariantCallFile, recordCountUncompressed){
vcflib::VariantCallFile variantFile;
std::string filename = "../samples/sample.vcf";
variantFile.open(filename);
vcflib::Variant var(variantFile);
long int count = 0;
while (variantFile.getNextVariant(var)) {
count+= 1;
}
ASSERT_EQ(count, 9);
}
TEST(VariantCallFile, recordCountCompressed){
vcflib::VariantCallFile variantFile;
std::string filename = "../samples/sample.compressed.vcf.gz";
variantFile.open(filename);
vcflib::Variant var(variantFile);
long int count = 0;
while (variantFile.getNextVariant(var)) {
count+= 1;
}
ASSERT_EQ(count, 9);
}
TEST(VariantCallFile, sampleNamesCompressed){
vcflib::VariantCallFile variantFile;
std::string filename = "../samples/sample.compressed.vcf.gz";
variantFile.open(filename);
int sampleSize = variantFile.sampleNames.size();
ASSERT_EQ(sampleSize, 3);
std::vector<std::string> names;
names.push_back("NA00001");
names.push_back("NA00002");
names.push_back("NA00003");
int counter = 0;
for(std::vector<std::string>::iterator it
= variantFile.sampleNames.begin();
it != variantFile.sampleNames.end(); it++){
ASSERT_EQ(*it, names[counter]);
counter+=1;
}
}
|
