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Determines if it is a BAM/SAM file by reading the beginning of the file.
Determines if it is a BAM/SAM file by reading the beginning of the file.
Returns true if successfully opened reading, false if not.
Returns true if successfully opened reading, false if not.
|-
| bool IsEOF()
| bool: true if the end of file has been reached, false if not.
|-
|-
| bool OpenForWrite(const char * filename)
| bool OpenForWrite(const char * filename)
SamRecord samRecord;
SamRecord samRecord;
// Keep reading records until it fails.
// Keep reading records until the end of the file is reached.
int recordCount = 0;
int numValidRecords = 0;
while (samIn.ReadRecord(samHeader, samRecord) == true)
int numRecords = 0;
while(!samIn.IsEOF())
{
{
if(samIn.ReadRecord(samHeader, samRecord) == true)
{
numRecords++;
// Successfully read a record from the file, so check to see
// if it is valid.
if(samRecord.isValid())
{
// It is valid, so write it.
numValidRecords++;
samOut.WriteRecord(samHeader, samRecord);
}
}
}
}
std::cout << "Number of records = " << numRecords << std::endl;
std::cout << "Number of valid records = " << numValidRecords << std::endl;
}
}
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|-
| void resetRecord()
| Resets the record to be an empty record. This is not necessary when you are reading a Sam/Bam file, but if you are setting fields, it is a good idea to clean out a record before reusing it. Clearing it allows you to not have to set any empty fields.
|-
|-
| bool setReadName(const char* readName)
| bool setReadName(const char* readName)
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|-
| bool isValid()
| Returns true if the record is valid. This performs validation steps. TODO: the method exists, but it does not yet perform any checks, so just returns true.
|-
|-
| int getBlockSize()
| int getBlockSize()
