-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathbgzf.go
61 lines (51 loc) · 1.81 KB
/
bgzf.go
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
/* Copyright (C) 2016 Philipp Benner
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package gonetics
/* -------------------------------------------------------------------------- */
import "fmt"
import "io"
import "compress/gzip"
import "encoding/binary"
/* -------------------------------------------------------------------------- */
type BgzfExtra struct {
SI1 uint8
SI2 uint8
SLen uint16
BSize uint16
}
type BgzfReader struct {
gzip.Reader
}
/* -------------------------------------------------------------------------- */
func NewBgzfReader(r io.Reader) (*BgzfReader, error) {
if reader, err := gzip.NewReader(r); err != nil {
return nil, err
} else {
return &BgzfReader{Reader: *reader}, nil
}
}
/* -------------------------------------------------------------------------- */
func (reader *BgzfReader) GetExtra() (*BgzfExtra, error) {
if len(reader.Header.Extra) != 6 {
return nil, fmt.Errorf("no extra information available")
}
extra := BgzfExtra{}
extra.SI1 = reader.Header.Extra[0]
extra.SI2 = reader.Header.Extra[1]
extra.SLen = binary.LittleEndian.Uint16(reader.Header.Extra[2:4])
extra.BSize = binary.LittleEndian.Uint16(reader.Header.Extra[4:6])
return &extra, nil
}