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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"
#include "SamFlag.h"
#include "Modify.h"
void testModify()
{
modify modTest;
modTest.testModify("testFiles/testSam.sam");
#ifdef __ZLIB_AVAILABLE__
modTest.testModify("testFiles/testBam.bam");
#endif
}
void modify::testModify(const char* filename)
{
myFilename = filename;
modifyPosition();
modifyCigar();
modifyFlag();
modifyTags();
}
void modify::modifyPosition()
{
openAndRead1Rec();
// Verify the initial bin.
assert(samRecord.getBin() == 4681);
// Change the position and verify that the bin is updated.
assert(samRecord.set0BasedPosition(33768));
// Verify the bin was updated.
assert(samRecord.getBin() == 4683);
assert(samRecord.get0BasedPosition() == 33768);
}
void modify::modifyCigar()
{
openAndRead1Rec();
// Verify the initial bin.
assert(samRecord.getBin() == 4681);
// Change the Cigar such that it modifies the bin.
assert(samRecord.setCigar("33768M"));
// Verify the bin was updated.
assert(samRecord.getBin() == 585);
}
void modify::modifyFlag()
{
openAndRead1Rec();
// Verify the initial bin.
uint16_t flag = 73;
assert(samRecord.getFlag() == flag);
SamFlag::setDuplicate(flag);
assert(flag == 1097);
assert(samRecord.setFlag(flag));
assert(samRecord.getFlag() == 1097);
SamFlag::setNotDuplicate(flag);
assert(flag == 73);
assert(samRecord.setFlag(flag));
assert(samRecord.getFlag() == 73);
}
void modify::openAndRead1Rec()
{
// Open the file for reading.
assert(samIn.OpenForRead(myFilename.c_str()));
// Read the sam header.
assert(samIn.ReadHeader(samHeader));
// Read the first record.
assert(samIn.ReadRecord(samHeader, samRecord));
}
void modify::modifyTags()
{
assert(samIn.OpenForRead(myFilename.c_str()));
// Read the sam header.
assert(samIn.ReadHeader(samHeader));
SamFile samOut;
SamFile bamOut;
std::string inputType = myFilename.substr(myFilename.find_last_of('.'));
std::string outFileBase = "results/updateTagFrom";
if(inputType == ".bam")
{
outFileBase += "Bam";
}
else
{
outFileBase += "Sam";
}
std::string outFile = outFileBase + ".sam";
assert(samOut.OpenForWrite(outFile.c_str()));
outFile = outFileBase + ".bam";
assert(bamOut.OpenForWrite(outFile.c_str()));
assert(samOut.WriteHeader(samHeader));
assert(bamOut.WriteHeader(samHeader));
int count = 0;
// Read the records.
while(samIn.ReadRecord(samHeader, samRecord))
{
if(count == 0)
{
assert(samRecord.rmTag("MD", 'Z'));
}
else if(count == 2)
{
assert(samRecord.rmTags("XT:A;MD:Z;AB:c;NM:i"));
}
else if(count == 4)
{
assert(samRecord.rmTags("MD:Z,AB:c,NM:i"));
}
assert(bamOut.WriteRecord(samHeader, samRecord));
assert(samOut.WriteRecord(samHeader, samRecord));
++count;
}
}
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