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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 "ReadFiles.h"
#include "WriteFiles.h"
#include "ValidationTest.h"
#include "BamIndexTest.h"
#include "ModifyVar.h"
#include "Modify.h"
#include "SamFileTest.h"
#include "TestEquals.h"
#include "TestFilter.h"
#include "ShiftIndels.h"
#include "TestPileup.h"
#include "TestPosList.h"
#include "TestCigarHelper.h"
#include "TestSamRecordPool.h"
#include "TestSamCoordOutput.h"
#include "TestSamRecordHelper.h"
int main(int argc, char ** argv)
{
if(argc == 1)
{
testReadSam();
#ifdef __ZLIB_AVAILABLE__
testReadBam();
testReadBam();
#endif
testAddHeaderAndTagToFile("testFiles/testSam.sam",
"results/addedTagToSam.bam");
testAddHeaderAndTagToFile("testFiles/testSam.sam",
"results/addedTagToSam.sam");
// Can't read bams without zlib
#ifdef __ZLIB_AVAILABLE__
testAddHeaderAndTagToFile("testFiles/testBam.bam",
"results/addedTagToBam.sam");
testAddHeaderAndTagToFile("testFiles/testBam.bam",
"results/addedTagToBam.bam");
#endif
testValidateSortedRead();
testWrite();
testSamQNAME();
testBamRID();
testEmptyQual();
// Can't read bams without zlib
#ifdef __ZLIB_AVAILABLE__
testBamIndex();
#endif
testModifyVar();
testModify();
testSamFile();
testSeqEquals();
testFilter();
testShiftIndels();
testPileup();
testPosList();
testCigarHelper();
testSamRecordPool();
testSamCoordOutput();
testSamRecordHelper();
}
else
{
modifyFirstBaseLong();
}
}
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