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
|
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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/>.
*/
#ifndef __SAM_INTERFACE_H__
#define __SAM_INTERFACE_H__
#include "GenericSamInterface.h"
class SamInterface : public GenericSamInterface
{
public:
SamInterface();
~SamInterface();
// Reads the header section from the specified SAM file and stores it in
// the passed in header.
virtual bool readHeader(IFILE filePtr, SamFileHeader& header,
SamStatus& status);
// Writes the specified header into the specified SAM file.
virtual bool writeHeader(IFILE filePtr, SamFileHeader& header,
SamStatus& status);
// Reads the next record from the specified SAM file and stores it in
// the passed in record.
virtual void readRecord(IFILE filePtr,
SamFileHeader& header,
SamRecord& record,
SamStatus& samStatus);
// Writes the specified record into the specified SAM file.
virtual SamStatus::Status writeRecord(IFILE filePtr,
SamFileHeader& header,
SamRecord& record,
SamRecord::SequenceTranslation translation);
virtual bool isEOF(IFILE filePtr);
private:
void ParseHeaderLine(StringIntHash & tags, StringArray & values);
String buffer;
StringArray tokens;
// Store the first record as it is read when trying to read the
// header so it can be returned when a record is read.
// Clear after it has been processed.
String myFirstRecord;
};
#endif
|
