libStatGen Software  1
ReadFiles.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 #include "SamFile.h"
19 void testReadSam();
20 void testReadBam();
21 void testRead(SamFile &inSam);
22 
23 void testAddHeaderAndTagToFile(const char* inputName, const char* outputName);
24 
25 void testValidateSortedRead();
26 
27 void validateRead1ModQuality(SamRecord& samRecord);
28 
29 void testModHeader(SamFileHeader& samHeader);
30 
31 void testFlagRead(const char* fileName);
32 
33 void testCopyHeader(SamFileHeader& samHeader);
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:34
SamRecord
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:51
SamFile
Allows the user to easily read/write a SAM/BAM file.
Definition: SamFile.h:35