Validate.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 
00020 void validateRead1(SamRecord& samRecord);
00021 void validateRead2(SamRecord& samRecord);
00022 void validateRead3(SamRecord& samRecord);
00023 void validateRead4(SamRecord& samRecord);
00024 void validateRead5(SamRecord& samRecord);
00025 void validateRead6(SamRecord& samRecord);
00026 void validateRead7(SamRecord& samRecord);
00027 void validateRead8(SamRecord& samRecord);
00028 void validateRead9(SamRecord& samRecord);
00029 void validateRead10(SamRecord& samRecord);
00030 
00031 
00032 void validateHeader(SamFileHeader& samHeader);
00033 void validateHeaderFields(SamFileHeader& samHeader);
00034 void validateHeaderString(SamFileHeader& samHeader);
00035 
00036 class Validate
00037 {
00038 public:
00039     static const int READ1_POS = 1010;
00040     static const int READ1_ALIGN_END = 1016;
00041     static const int READ1_UNCLIP_START = 1010;
00042     static const int READ1_UNCLIP_END = 1016;
00043     static const int READ1_ALIGN_LEN = 7;
00044     static const std::string READ1_CIGAR;
00045     static const std::string READ1_SEQ;
00046     static const std::string READ1_QUAL;
00047 
00048     static const int READ2_POS = 1011;
00049 
00050     static const int READ6_POS = 1750;
00051     static const int READ6_ALIGN_END = 1754;
00052     static const int READ6_UNCLIP_START = 1745;
00053     static const int READ6_UNCLIP_END = 1754;
00054     static const int READ6_ALIGN_LEN = 5;
00055     static const std::string READ6_CIGAR;
00056     static const std::string READ6_SEQ;
00057     static const std::string READ6_QUAL;
00058 
00059     static const int READ7_POS = 1750;
00060     static const int READ7_ALIGN_END = 1754;
00061     static const int READ7_UNCLIP_START = 1747;
00062     static const int READ7_UNCLIP_END = 1758;
00063     static const int READ7_ALIGN_LEN = 5;
00064     static const std::string READ7_CIGAR;
00065     static const std::string READ7_SEQ;
00066     static const std::string READ7_QUAL;
00067 
00068 };