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
20void validateRead1(SamRecord& samRecord);
21void validateRead2(SamRecord& samRecord);
22void validateRead3(SamRecord& samRecord);
23void validateRead4(SamRecord& samRecord);
24void validateRead5(SamRecord& samRecord);
25void validateRead6(SamRecord& samRecord);
26void validateRead7(SamRecord& samRecord);
27void validateRead8(SamRecord& samRecord);
28void validateRead9(SamRecord& samRecord);
29void validateRead10(SamRecord& samRecord);
30
31
32void validateHeader(SamFileHeader& samHeader);
33void validateHeaderFields(SamFileHeader& samHeader);
34void validateHeaderString(SamFileHeader& samHeader);
35
37{
38public:
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};
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:35
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:52