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/*
* 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 testSeqEquals();
class EqualsTest
{
public:
enum FileType{SAM, BAM};
static void testEq(FileType inputType);
private:
static void reset();
static void validateEqRead(SamRecord& samRecord,
int readIndex,
const char* actualExpectedSequence);
static void validateEqReadBuffer(SamRecord& samRecord,
const char* expectedSequence);
static const char* READ_NAMES[];
static const char* READ_SEQS_BASES[];
static const char* READ_SEQS_EQUALS[];
static const char* READ_SEQS_MIXED[];
static const char* expectedReferenceName;
static const char* expectedMateReferenceName;
static const char* expectedMateReferenceNameOrEqual;
static const char* expectedCigar;
static const char* expectedQuality;
static std::vector<unsigned int> expectedCigarHex;
static int expected0BasedAlignmentEnd;
static int expected1BasedAlignmentEnd;
static int expectedAlignmentLength;
static int expected0BasedUnclippedStart;
static int expected1BasedUnclippedStart;
static int expected0BasedUnclippedEnd;
static int expected1BasedUnclippedEnd;
static bamRecordStruct expectedRecord;
};
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