ReadFiles.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 #include "SamFile.h"
00019 void testReadSam();
00020 void testReadBam();
00021 void testRead(SamFile &inSam);
00022 
00023 void testAddHeaderAndTagToFile(const char* inputName, const char* outputName);
00024 
00025 void testValidateSortedRead();
00026 
00027 void validateRead1ModQuality(SamRecord& samRecord);
00028 
00029 void testModHeader(SamFileHeader& samHeader);