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
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
|
package vcfgo
import (
"fmt"
"math"
"os"
"testing"
"bytes"
"strings"
. "gopkg.in/check.v1"
)
func Test(t *testing.T) { TestingT(t) }
type VCFSuite struct{}
var _ = Suite(&VCFSuite{})
var infotests = []struct {
input string
exp *Info
}{
{`##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">`,
&Info{Id: "NS", Number: "1", Type: "Integer", Description: "Number of Samples With Data"}},
{`##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">`,
&Info{Id: "DP", Number: "1", Type: "Integer", Description: "Total Depth"}},
{`##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">`,
&Info{Id: "AF", Number: "A", Type: "Float", Description: "Allele Frequency"}},
{`##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">`,
&Info{Id: "AA", Number: "1", Type: "String", Description: "Ancestral Allele"}},
{`##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">`,
&Info{Id: "DB", Number: "0", Type: "Flag", Description: "dbSNP membership, build 129"}},
{`##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">`,
&Info{Id: "H2", Number: "0", Type: "Flag", Description: "HapMap2 membership"}},
}
var formattests = []struct {
input string
exp *SampleFormat
}{
{`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`,
&SampleFormat{Id: "GT", Number: "1", Type: "String", Description: "Genotype"}},
{`##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">`,
&SampleFormat{Id: "GQ", Number: "1", Type: "Integer", Description: "Genotype Quality"}},
{`##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">`,
&SampleFormat{Id: "HQ", Number: "2", Type: "Integer", Description: "Haplotype Quality"}},
{`##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">`,
&SampleFormat{Id: "DP", Number: "1", Type: "Integer", Description: "Read Depth"}},
}
var filtertests = []struct {
filter string
exp []string
}{
{`##FILTER=<ID=q10,Description="Quality below 10">`,
[]string{"q10", "Quality below 10"}},
{`##FILTER=<ID=s50,Description="Less than 50% of samples have data">`,
[]string{"s50", "Less than 50% of samples have data"}},
}
var samplelinetests = []struct {
line string
exp []string
}{
{`#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003`, []string{"NA00001", "NA00002", "NA00003"}},
{`#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT`, []string{}},
}
func (s *VCFSuite) TestHeaderInfoParse(c *C) {
for _, v := range infotests {
obs, err := parseHeaderInfo(v.input)
c.Assert(err, IsNil)
c.Assert(obs, DeepEquals, v.exp)
c.Assert(obs.String(), Equals, v.input)
}
}
func (s *VCFSuite) TestHeaderFormatParse(c *C) {
for _, v := range formattests {
obs, err := parseHeaderFormat(v.input)
c.Assert(err, IsNil)
c.Assert(obs, DeepEquals, v.exp)
c.Assert(obs.String(), Equals, v.input)
}
}
func (s *VCFSuite) TestHeaderFilterParse(c *C) {
for _, v := range filtertests {
obs, err := parseHeaderFilter(v.filter)
c.Assert(err, IsNil)
c.Assert(obs, DeepEquals, v.exp)
}
}
func (s *VCFSuite) TestHeaderVersionParse(c *C) {
obs, err := parseHeaderFileVersion(`##fileformat=VCFv4.2`)
c.Assert(err, IsNil)
c.Assert(obs, Equals, "4.2")
}
func (s *VCFSuite) TestHeaderBadVersionParse(c *C) {
_, err := parseHeaderFileVersion(`##fileformat=VFv4.2`)
c.Assert(err, ErrorMatches, "file format error.*")
}
func (s *VCFSuite) TestHeaderContigParse(c *C) {
m, err := parseHeaderContig(`##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>`)
c.Assert(err, IsNil)
c.Assert(m, DeepEquals, map[string]string{"assembly": "B36", "md5": "f126cdf8a6e0c7f379d618ff66beb2da", "species": "\"Homo sapiens\"", "taxonomy": "x", "ID": "20", "length": "62435964"})
}
func (s *VCFSuite) TestHeaderExtra(c *C) {
obs, err := parseHeaderExtraKV("##key=value")
c.Assert(err, IsNil)
c.Assert(obs[0], Equals, "key")
c.Assert(obs[1], Equals, "value")
}
func (s *VCFSuite) TestHeaderSampleLine(c *C) {
for _, v := range samplelinetests {
r, err := parseSampleLine(v.line)
c.Assert(err, IsNil)
c.Assert(r, DeepEquals, v.exp)
}
}
func (s *VCFSuite) TestIssue5(c *C) {
rdr, err := os.Open("test-multi-allelic.vcf")
c.Assert(err, IsNil)
vcf, err := NewReader(rdr, false)
c.Assert(err, IsNil)
variant := vcf.Read()
samples := variant.Samples
c.Assert(samples[0].GT, DeepEquals, []int{2, 2})
c.Assert(samples[1].GT, DeepEquals, []int{2, 2})
c.Assert(samples[2].GT, DeepEquals, []int{2, 2})
}
func (s *VCFSuite) TestWriterNoSamples(c *C) {
fname := "test-no-samples-writer.vcf"
rdr, err := os.Open(fname)
c.Assert(err, IsNil)
vcf, err := NewReader(rdr, false)
c.Assert(err, IsNil)
var wtr bytes.Buffer
_, err = NewWriter(&wtr, vcf.Header)
c.Assert(err, IsNil)
str := wtr.String()
c.Assert(strings.Contains(str, "\tFORMAT"), Equals, false)
}
func (s *VCFSuite) TestWriterWithSamples(c *C) {
fname := "test-h.vcf"
rdr, err := os.Open(fname)
c.Assert(err, IsNil)
vcf, err := NewReader(rdr, false)
c.Assert(err, IsNil)
var wtr bytes.Buffer
_, err = NewWriter(&wtr, vcf.Header)
c.Assert(err, IsNil)
str := wtr.String()
c.Assert(strings.Contains(str, "\tFORMAT"), Equals, true)
lines := strings.Split(strings.TrimSpace(str), "\n")
c.Assert(strings.HasPrefix(lines[len(lines)-1], "#CHROM"), Equals, true)
}
func (s *VCFSuite) TestIssue20SampleGenotypes(c *C) {
fname := "test-issue-20.vcf"
rdr, err := os.Open(fname)
c.Assert(err, IsNil)
defer rdr.Close()
vcf, err := NewReader(rdr, false)
c.Assert(err, IsNil)
variant := vcf.Read()
c.Assert(variant, NotNil)
samples := variant.Samples
c.Assert(len(samples), Equals, 3)
// print samples
fmt.Printf("%+v\n", samples)
// Check genotypes for each sample
c.Assert(samples[0].GT, DeepEquals, []int{1, 1})
c.Assert(samples[1].GT, DeepEquals, []int{0, 1})
c.Assert(samples[2].GT, DeepEquals, []int{-1, -1})
}
func (s *VCFSuite) TestReadWriteQual(c *C) {
vcfContent := `##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 123 . A C . PASS .
`
rdr := strings.NewReader(vcfContent)
vcf, err := NewReader(rdr, false)
c.Assert(err, IsNil)
variant := vcf.Read()
c.Assert(variant, NotNil)
c.Assert(math.Float32bits(variant.Quality), Equals, math.Float32bits(MISSING_VAL))
var wtr bytes.Buffer
w, err := NewWriter(&wtr, vcf.Header)
c.Assert(err, IsNil)
w.WriteVariant(variant)
c.Assert(strings.Contains(wtr.String(), "\t.\tPASS"), Equals, true)
}
|
