SamRecordHelperTest Class Reference

Static Public Member Functions
static void	testSamRecordHelper (const char *fileName)

Detailed Description

Definition at line 21 of file TestSamRecordHelper.h.

Member Function Documentation

testSamRecordHelper()

void SamRecordHelperTest::testSamRecordHelper ( const char * fileName )

static

Definition at line 31 of file TestSamRecordHelper.cpp.

{
    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);
  
}

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The documentation for this class was generated from the following files:

• bam/test/TestSamRecordHelper.h
• bam/test/TestSamRecordHelper.cpp