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
|
// +build ignore
// Copyright ©2017 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package cram
import (
"bytes"
"errors"
"fmt"
"io/ioutil"
"net/http"
"reflect"
"testing"
"github.com/kortschak/utter"
)
func TestReadDefinition(t *testing.T) {
tests := []struct {
bytes [26]byte
want definition
err error
}{
{
bytes: [26]byte{
'C', 'R', 'A', 'M',
3,
0,
's', 'h', 'a', '1', '-', '0',
},
want: definition{
Magic: [4]byte{'C', 'R', 'A', 'M'},
Version: [2]byte{3, 0},
ID: [20]byte{'s', 'h', 'a', '1', '-', '0'},
},
err: nil,
},
{
bytes: [26]byte{
'B', 'A', 'M', 0x1,
3,
0,
's', 'h', 'a', '1', '-', '0',
},
want: definition{
Magic: [4]byte{'B', 'A', 'M', 0x1},
Version: [2]byte{3, 0},
ID: [20]byte{'s', 'h', 'a', '1', '-', '0'},
},
err: errors.New(`cram: not a cram file: magic bytes "BAM\x01"`),
},
}
for _, test := range tests {
var got definition
err := got.readFrom(bytes.NewReader(test.bytes[:]))
if fmt.Sprint(err) != fmt.Sprint(test.err) {
t.Errorf("unexpected error return: got: %q want: %q", err, test.err)
}
if got != test.want {
t.Errorf("unexpected cram definition value:\ngot: %#v\nwant:%#v", got, test.want)
}
}
}
func TestReadEOFContainer(t *testing.T) {
var c Container
err := c.readFrom(bytes.NewReader(cramEOFmarker))
if err != nil {
t.Errorf("failed to read container: %v\n%#v", err, c)
}
var b Block
err = b.readFrom(c.blockData)
if err != nil {
t.Errorf("failed to read block: %v\n%#v", err, b)
}
c.blockData = nil
wantContainer := Container{
blockLen: 15,
refID: -1,
start: 4542278,
span: 0,
nRec: 0,
recCount: 0,
bases: 0,
blocks: 1,
landmarks: nil,
crc32: 0x4fd9bd05,
}
if !reflect.DeepEqual(c, wantContainer) {
t.Errorf("unexpected EOF container value:\ngot: %#v\nwant:%#v", c, wantContainer)
}
wantBlock := Block{
method: rawMethod,
typ: compressionHeader,
contentID: 0,
compressedSize: 6,
rawSize: 6,
blockData: []byte{0x01, 0x00, 0x01, 0x00, 0x01, 0x00},
crc32: 0x4b0163ee,
}
if !reflect.DeepEqual(b, wantBlock) {
t.Errorf("unexpected EOF block value:\ngot: %#v\nwant:%#v", b, wantBlock)
}
}
func TestHasEOF(t *testing.T) {
r, err := get(`https://github.com/samtools/htslib/blob/develop/test/ce%235b_java.cram?raw=true`)
if err != nil {
t.Fatalf("failed to open test file: %v", err)
}
hasEOF, err := HasEOF(r)
if err != nil {
t.Fatalf("failed to read EOF: %v", err)
}
if !hasEOF {
t.Error("failed to identify known EOF block")
}
}
func TestRead(t *testing.T) {
utter.Config.BytesWidth = 8
r, err := get(`https://github.com/samtools/htslib/blob/develop/test/ce%235b_java.cram?raw=true`)
if err != nil {
t.Fatalf("failed to open test file: %v", err)
}
cr, err := NewReader(r)
if err != nil {
t.Fatalf("failed to read definition: %v\n%#v", err, cr.d)
}
wantDefinition := definition{
Magic: [4]uint8{
0x43, 0x52, 0x41, 0x4d, // |CRAM|
},
Version: [2]byte{3, 0},
ID: [20]byte{
0x63, 0x65, 0x23, 0x35, 0x62, 0x2e, 0x73, 0x61, // |ce#5b.sa|
0x6d, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, // |m.......|
0x00, 0x00, 0x00, 0x00, /* */ // |....|
},
}
t.Log(utter.Sdump(cr.d))
if cr.d != wantDefinition {
t.Errorf("unexpected cram definition:\ngot: %#v\nwant:%#v", cr.d, wantDefinition)
}
for cr.Next() {
c := cr.Container()
blockData := c.blockData
c.blockData = nil
t.Log(utter.Sdump(c))
c.blockData = blockData
for c.Next() {
v, err := c.Block().Value()
if err != nil {
t.Errorf("failed to get value: %v", err)
}
t.Log(utter.Sdump(v))
}
if c.Err() != nil {
t.Errorf("failed to read block: %v\n%#v", err, c.block)
}
}
if cr.Err() != nil {
t.Fatalf("failed to read container: %v\n%#v", err, cr.c)
}
}
func get(url string) (*bytes.Reader, error) {
resp, err := http.Get(url)
if err != nil {
return nil, err
}
defer resp.Body.Close()
b, err := ioutil.ReadAll(resp.Body)
if err != nil {
return nil, err
}
return bytes.NewReader(b), nil
}
|
