3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Usage Example
// Read the first sam record.
// Read the first sam record.
SamRecord samRecord;
SamRecord samRecord;
// Track if any of the records are invalid. Initialize to 0, it will
// be set to -1 on an invalid record.
int status = 0;
// Keep reading records until the end of the file is reached.
// Keep reading records until the end of the file is reached.
int numValidRecords = 0;
int numValidRecords = 0;
while(!samIn.IsEOF())
while(!samIn.IsEOF())
{
{
if(samIn.ReadRecord(samHeader, samRecord) == true)
if(samIn.ReadRecord(samHeader, samRecord) == true)
{
{
// Successfully read a record from the file, so check to see
// Successfully read a record from the file, so check to see
// if it is valid.
// if it is valid.
numValidRecords++;
numValidRecords++;
samOut.WriteRecord(samHeader, samRecord);
samOut.WriteRecord(samHeader, samRecord);
}
else
{
// There is at least one invalid record, return -1.
status = -1;
}
}
else
{
// Failed to read the record. Check to see if it failed due to
// there being no more records, which is not a failure. Any
// other failure reason counts as a failure.
if(samIn.GetFailure() != SamStatus::NO_MORE_RECS)
{
// Read failed, invalid.
status = -1;
}
}
}
}
}
}
std::cout << "Number of records = " << numRecords << std::endl;
std::cout << "Number of records read = " <<
samIn.GetCurrentRecordCount() << std::endl;
std::cout << "Number of records written = " <<
samOut.GetCurrentRecordCount() << std::endl;
std::cout << "Number of valid records = " << numValidRecords << std::endl;
std::cout << "Number of valid records = " << numValidRecords << std::endl;
return(status);
}
}
</source>
</source>
== Reading Indexed (and Sorted) BAM Files ==
== Reading Indexed (and Sorted) BAM Files ==
