Modify.h

00001 /*
00002  *  Copyright (C) 2010  Regents of the University of Michigan
00003  *
00004  *   This program is free software: you can redistribute it and/or modify
00005  *   it under the terms of the GNU General Public License as published by
00006  *   the Free Software Foundation, either version 3 of the License, or
00007  *   (at your option) any later version.
00008  *
00009  *   This program is distributed in the hope that it will be useful,
00010  *   but WITHOUT ANY WARRANTY; without even the implied warranty of
00011  *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00012  *   GNU General Public License for more details.
00013  *
00014  *   You should have received a copy of the GNU General Public License
00015  *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
00016  */
00017 
00018 void testModify();
00019 
00020 class modify
00021 {
00022 public:
00023     void testModify(const char* filename);
00024    
00025 private:
00026     void modifyPosition();
00027 
00028     void modifyCigar();
00029 
00030     // Open and read the first record.
00031     void openAndRead1Rec();
00032 
00033     void modifyTags();
00034 
00035     // Variables.
00036     std::string myFilename;
00037 
00038     // Rather than passing around all these variables, just store them in the class.
00039     SamFile samIn;
00040     SamFileHeader samHeader;
00041     SamRecord samRecord;
00042 };