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TestValidate.h
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "SamFile.h"
void validateRead1(SamRecord& samRecord);
void validateRead2(SamRecord& samRecord);
void validateRead3(SamRecord& samRecord);
void validateRead4(SamRecord& samRecord);
void validateRead5(SamRecord& samRecord);
void validateRead6(SamRecord& samRecord);
void validateRead7(SamRecord& samRecord);
void validateRead8(SamRecord& samRecord);
void validateRead9(SamRecord& samRecord);
void validateRead10(SamRecord& samRecord);
void validateHeader(SamFileHeader& samHeader);
void validateHeaderFields(SamFileHeader& samHeader);
void validateHeaderString(SamFileHeader& samHeader);
class TestValidate
{
public:
static const int READ1_POS = 1010;
static const int READ1_ALIGN_END = 1016;
static const int READ1_UNCLIP_START = 1010;
static const int READ1_UNCLIP_END = 1016;
static const int READ1_ALIGN_LEN = 7;
static const std::string READ1_CIGAR;
static const std::string READ1_SEQ;
static const std::string READ1_QUAL;
static const int READ2_POS = 1011;
static const int READ6_POS = 1750;
static const int READ6_ALIGN_END = 1754;
static const int READ6_UNCLIP_START = 1745;
static const int READ6_UNCLIP_END = 1754;
static const int READ6_ALIGN_LEN = 5;
static const std::string READ6_CIGAR;
static const std::string READ6_SEQ;
static const std::string READ6_QUAL;
static const int READ7_POS = 1750;
static const int READ7_ALIGN_END = 1754;
static const int READ7_UNCLIP_START = 1747;
static const int READ7_UNCLIP_END = 1758;
static const int READ7_ALIGN_LEN = 5;
static const std::string READ7_CIGAR;
static const std::string READ7_SEQ;
static const std::string READ7_QUAL;
};
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
TestValidate
Definition TestValidate.h:37