libStatGen Software  1
TestValidate.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 
20 void validateRead1(SamRecord& samRecord);
21 void validateRead2(SamRecord& samRecord);
22 void validateRead3(SamRecord& samRecord);
23 void validateRead4(SamRecord& samRecord);
24 void validateRead5(SamRecord& samRecord);
25 void validateRead6(SamRecord& samRecord);
26 void validateRead7(SamRecord& samRecord);
27 void validateRead8(SamRecord& samRecord);
28 void validateRead9(SamRecord& samRecord);
29 void validateRead10(SamRecord& samRecord);
30 
31 
32 void validateHeader(SamFileHeader& samHeader);
33 void validateHeaderFields(SamFileHeader& samHeader);
34 void validateHeaderString(SamFileHeader& samHeader);
35 
37 {
38 public:
39  static const int READ1_POS = 1010;
40  static const int READ1_ALIGN_END = 1016;
41  static const int READ1_UNCLIP_START = 1010;
42  static const int READ1_UNCLIP_END = 1016;
43  static const int READ1_ALIGN_LEN = 7;
44  static const std::string READ1_CIGAR;
45  static const std::string READ1_SEQ;
46  static const std::string READ1_QUAL;
47 
48  static const int READ2_POS = 1011;
49 
50  static const int READ6_POS = 1750;
51  static const int READ6_ALIGN_END = 1754;
52  static const int READ6_UNCLIP_START = 1745;
53  static const int READ6_UNCLIP_END = 1754;
54  static const int READ6_ALIGN_LEN = 5;
55  static const std::string READ6_CIGAR;
56  static const std::string READ6_SEQ;
57  static const std::string READ6_QUAL;
58 
59  static const int READ7_POS = 1750;
60  static const int READ7_ALIGN_END = 1754;
61  static const int READ7_UNCLIP_START = 1747;
62  static const int READ7_UNCLIP_END = 1758;
63  static const int READ7_ALIGN_LEN = 5;
64  static const std::string READ7_CIGAR;
65  static const std::string READ7_SEQ;
66  static const std::string READ7_QUAL;
67 
68 };
TestValidate
Definition: TestValidate.h:37
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:35
SamRecord
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:52