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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/>.
*/
void modifyFirstBase();
void modifyFirstBaseLong();
void testModifyVar();
class modifyVar
{
public:
void testModifyVar(const char* filename, bool valBufFirst);
private:
void testModifyReadNameOnlySameLength();
void testModifyCigarOnlySameLength();
void testModifySequenceOnlySameLength();
void testModifyQualityOnlySameLength();
void testRemoveQuality();
void testShortenQuality();
void testLengthenQuality();
void testShortenReadName();
void testShortenCigar();
void testShortenSequence();
void testLengthenReadName();
void testLengthenCigar();
void testLengthenSequence();
void testRemoveCigar();
void testRemoveSequence();
void testLengthenSequenceAndQuality();
void validate();
void validateReadName(const bamRecordStruct* recordBuffer);
void validateCigar(const bamRecordStruct* recordBuffer);
void validateSequence(const bamRecordStruct* recordBuffer);
void validateQuality(const bamRecordStruct* recordBuffer);
void validateTags(const bamRecordStruct* recordBuffer);
void validateReadNameString();
void validateCigarString();
void validateSequenceString();
void validateQualityString();
void validateTagsString();
// Open and read the first record.
void openAndRead1Rec();
void resetExpected();
// Variables.
const char* myFilename;
bool myValBufFirst;
// Rather than passing around all these variables, just store them in the class.
SamFile samIn;
SamFileHeader samHeader;
SamRecord samRecord;
const bamRecordStruct* recordBuffer;
// Expected values.
int expectedCigarBufLen;
unsigned int expectedCigarBuffer[100];
unsigned char expectedSequenceBuffer[100];
int expectedTagsLen;
unsigned char expectedTagsBuffer[100];
// Expected values for the strings.
std::string expectedReadNameString;
std::string expectedCigarString;
std::string expectedSequenceString;
std::string expectedQualityString;
};
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