libStatGen Software 1
BamInterface.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 __BAM_INTERFACE_H__
19#define __BAM_INTERFACE_H__
20
21#include "GenericSamInterface.h"
22
24{
25public:
28
29 // Reads the header section from the specified BAM file and stores it in
30 // the passed in header.
31 // Returns false and updates the status on failure.
32 virtual bool readHeader(IFILE filePtr, SamFileHeader& header,
33 SamStatus& samStatus);
34
35 // Writes the specified header into the specified BAM file.
36 // Returns false and updates the status on failure.
37 virtual bool writeHeader(IFILE filePtr, SamFileHeader& header,
38 SamStatus& samStatus);
39
40 // Reads the next record from the specified BAM file and stores it in
41 // the passed in record.
42 virtual void readRecord(IFILE filePtr,
43 SamFileHeader& header,
44 SamRecord& record,
45 SamStatus& samStatus);
46
47 // Writes the specified record into the specified BAM file.
48 virtual SamStatus::Status writeRecord(IFILE filePtr,
49 SamFileHeader& header,
50 SamRecord& record,
52
53private:
54
55};
56
57#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