libStatGen Software 1
GenericSamInterface.h
1/*
2 * Copyright (C) 2010 Regents of the University of Michigan
3 *
4 * This program is free software: you can redistribute it and/or modify
5 * it under the terms of the GNU General Public License as published by
6 * the Free Software Foundation, either version 3 of the License, or
7 * (at your option) any later version.
8 *
9 * This program is distributed in the hope that it will be useful,
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 * GNU General Public License for more details.
13 *
14 * You should have received a copy of the GNU General Public License
15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
16 */
17
18#ifndef __GENERIC_SAM_INTERFACE_H__
19#define __GENERIC_SAM_INTERFACE_H__
20
21#include "SamStatus.h"
22#include "InputFile.h"
23#include "SamFileHeader.h"
24#include "SamRecord.h"
25
27{
28public:
30 virtual ~GenericSamInterface();
31
32 // Pure virtual method that reads the header section from the specified file
33 // and stores it in the passed in header, returns false and sets the status
34 // on failure.
35 // Will be implemented specifically for sam/bam files.
36 virtual bool readHeader(IFILE filePtr, SamFileHeader& header,
37 SamStatus& status) = 0;
38
39 // Pure virtual method that writes the specified header into the specified
40 // file, returns false and sets the status on failure.
41 // Will be implemented specifically for sam/bam files.
42 virtual bool writeHeader(IFILE filePtr, SamFileHeader& header,
43 SamStatus& status) = 0;
44
45 // Pure virtual method that reads the next record from the specified file
46 // and stores it in the passed in record.
47 // Will be implemented specifically for sam/bam files.
48 // TODO On error, a more detailed message is appended to statusMsg.
49 virtual void readRecord(IFILE filePtr, SamFileHeader& header,
50 SamRecord& record,
51 SamStatus& samStatus) = 0;
52
53 // Pure virtual method that writes the specified record into the specified
54 // file.
55 // Will be implemented specifically for sam/bam files.
56 virtual SamStatus::Status writeRecord(IFILE filePtr, SamFileHeader& header,
57 SamRecord& record,
58 SamRecord::SequenceTranslation translation) = 0;
59
60 virtual bool isEOF(IFILE filePtr);
61};
62
63#endif
Class for easily reading/writing files without having to worry about file type (uncompressed,...
Definition: InputFile.h:37
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:35
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:52
SequenceTranslation
Enum containing the settings on how to translate the sequence if a reference is available.
Definition: SamRecord.h:57
This class is used to track the status results of some methods in the BAM classes.
Definition: StatGenStatus.h:27
Status
Return value enum for StatGenFile methods.
Definition: StatGenStatus.h:32