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/*
* Copyright (C) 2011 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 "TestFilter.h"
#include "TestValidate.h"
#include "SamFilter.h"
#include <assert.h>
void testFilter()
{
// Call generic test which since the sam and bam are identical, should
// contain the same results.
FilterTest::testFilter(FilterTest::SAM);
#ifdef __ZLIB_AVAILABLE__
FilterTest::testFilter(FilterTest::BAM);
#endif
}
void FilterTest::testFilter(FileType inputType)
{
SamFile inSam;
if(inputType == SAM)
{
assert(inSam.OpenForRead("testFiles/testSam.sam"));
}
else
{
assert(inSam.OpenForRead("testFiles/testBam.bam"));
}
// Read the SAM Header.
SamFileHeader samHeader;
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
SamRecord samRecord;
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead1(samRecord);
// Clip the read, 2 from the front and 2 from the back, which causes 2D to
// be dropped.
assert(SamFilter::softClip(samRecord, 2, 2) == SamFilter::CLIPPED);
assert(samRecord.get0BasedPosition() == TestValidate::READ1_POS + 2);
std::string expectedCigar = "2S1M2S";
assert(samRecord.getCigar() == expectedCigar);
assert(samRecord.getSequence() == TestValidate::READ1_SEQ);
assert(samRecord.getQuality() == TestValidate::READ1_QUAL);
// Only 1 base, so the end is the same as start
assert(samRecord.get0BasedAlignmentEnd() == TestValidate::READ1_POS + 2);
assert(samRecord.getAlignmentLength() == 1);
assert(samRecord.get0BasedUnclippedStart() == TestValidate::READ1_UNCLIP_START);
// The new unclipped end is not the same as the original end because the
// 2 deletions are lost.
assert(samRecord.get0BasedUnclippedEnd() == TestValidate::READ1_UNCLIP_END - 2);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead2(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead3(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead4(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead5(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead6(samRecord);
// Clip the read 2 more from the front and 2 from the back.
assert(SamFilter::softClip(samRecord, 5, 2) == SamFilter::CLIPPED);
assert(samRecord.get0BasedPosition() == TestValidate::READ6_POS + 2);
expectedCigar = "2H5S1M2S";
assert(samRecord.getCigar() == expectedCigar);
assert(samRecord.getSequence() == TestValidate::READ6_SEQ);
assert(samRecord.getQuality() == TestValidate::READ6_QUAL);
// Only 1 base, so the end is the same as start
assert(samRecord.get0BasedAlignmentEnd() == TestValidate::READ6_POS + 2);
assert(samRecord.getAlignmentLength() == 1);
assert(samRecord.get0BasedUnclippedStart() == TestValidate::READ6_UNCLIP_START);
assert(samRecord.get0BasedUnclippedEnd() == TestValidate::READ6_UNCLIP_END);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead7(samRecord);
// Clip the read 2 more from the front and 2 morefrom the back.
assert(SamFilter::softClip(samRecord, 5, 3) == SamFilter::CLIPPED);
assert(samRecord.get0BasedPosition() == TestValidate::READ7_POS + 2);
expectedCigar = "5S1M3S3H";
assert(samRecord.getCigar() == expectedCigar);
assert(samRecord.getSequence() == TestValidate::READ7_SEQ);
assert(samRecord.getQuality() == TestValidate::READ7_QUAL);
// Only 1 base, so the end is the same as start
assert(samRecord.get0BasedAlignmentEnd() == TestValidate::READ7_POS + 2);
assert(samRecord.getAlignmentLength() == 1);
assert(samRecord.get0BasedUnclippedStart() == TestValidate::READ7_UNCLIP_START);
assert(samRecord.get0BasedUnclippedEnd() == TestValidate::READ7_UNCLIP_END);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead8(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead9(samRecord);
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead10(samRecord);
}
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