libStatGen Software  1
Modify.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 void testModify();
19 
20 class modify
21 {
22 public:
23  void testModify(const char* filename);
24 
25 private:
26  void modifyPosition();
27 
28  void modifyCigar();
29 
30  void modifyFlag();
31 
32  // Open and read the first record.
33  void openAndRead1Rec();
34 
35  void modifyTags();
36 
37  // Variables.
38  std::string myFilename;
39 
40  // Rather than passing around all these variables, just store them in the class.
41  SamFile samIn;
42  SamFileHeader samHeader;
43  SamRecord samRecord;
44 };
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:35
Allows the user to easily read/write a SAM/BAM file.
Definition: SamFile.h:36
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:52
Definition: Modify.h:21