TestSamRecordHelper.cpp
/*
* Copyright (C) 2012 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 "TestSamRecordHelper.h"
#include "TestValidate.h"
#include "SamRecordHelper.h"
#include <assert.h>
void testSamRecordHelper()
{
// Call generic test.
SamRecordHelperTest::testSamRecordHelper("testFiles/testSam.sam");
// SamRecordHelperTest::testSamRecordHelper("testFiles/testBam.bam");
}
void SamRecordHelperTest::testSamRecordHelper(const char* fileName)
{
SamFile inSam;
assert(inSam.OpenForRead(fileName));
SamFileHeader samHeader;
assert(inSam.ReadHeader(samHeader));
validateHeader(samHeader);
SamRecord samRecord;
assert(inSam.ReadRecord(samHeader, samRecord) == true);
validateRead1(samRecord);
// Validate the entire sequence matches.
assert(SamRecordHelper::checkSequence(samRecord,
TestValidate::READ1_POS,
TestValidate::READ1_SEQ.c_str()) == 0);
// The read start position is 1010.
// The sequence is CCGAA.
assert(SamRecordHelper::checkSequence(samRecord, 1010, "CCGAA") == 0);
// Test not matching.
assert(SamRecordHelper::checkSequence(samRecord, 1010, "NNNNN") == -1);
// Test match, but not at the start.
assert(SamRecordHelper::checkSequence(samRecord, 1011, "CGA") == 1);
// Test match not at the start, but to the end.
assert(SamRecordHelper::checkSequence(samRecord, 1011, "CGAA") == 1);
// Test run over the end.
assert(SamRecordHelper::checkSequence(samRecord, 1011, "CGAAC") == -1);
}
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition: SamFileHeader.h:35
SamFile
Allows the user to easily read/write a SAM/BAM file.
Definition: SamFile.h:36
SamFile::ReadHeader
bool ReadHeader(SamFileHeader &header)
Reads the header section from the file and stores it in the passed in header.
Definition: SamFile.cpp:450
SamFile::ReadRecord
bool ReadRecord(SamFileHeader &header, SamRecord &record)
Reads the next record from the file & stores it in the passed in record.
Definition: SamFile.cpp:514
SamFile::OpenForRead
bool OpenForRead(const char *filename, SamFileHeader *header=NULL)
Open a sam/bam file for reading with the specified filename, determing the type of file and SAM/BAM b...
Definition: SamFile.cpp:93
SamRecordHelper::checkSequence
static int checkSequence(SamRecord &record, int32_t pos0Based, const char *sequence)
Helper method that checks if the record's read sequence starting at the specified 0-based reference p...
Definition: SamRecordHelper.cpp:21
SamRecord
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:52