LibStatGen: BAM

SAM/BAM File

Reading/Writing SAM/BAM Files

The SamFile class allows a user to easily read/write a SAM/BAM file. This methods found in this class are:

SamFile Class Methods

Method Name	Description
bool OpenForRead(const char* filename)	Opens the specified file for reading. Determines if it is a BAM/SAM file by reading the beginning of the file. Returns true if successfully opened reading, false if not.
bool OpenForWrite(const char * filename)	bool: true if successfully opened, false if not. Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file. Returns true if successfully opened for writing, false if not.
bool ReadHeader(SamFileHeader& header)	Reads the header section from the file and stores it in the passed in header. Returns true if successfully read, false if not.
bool WriteHeader(const SamFileHeader& header)	Writes the specified header into the file. Returns true if successfully written, false if not.
bool ReadRecord(SamFileHeader& header, SamRecord& record)	Reads the next record from the file and stores it in the passed in record. Returns true if successfully read, false if not.
bool WriteRecord(SamFileHeader& header, SamRecord& record)	Writes the specified record into the file. Returns true if successfully written, false if not.

Usage Example

The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the SamFile class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.

int main(int argc, char ** argv)
{
   if(argc != 3)
   {
      printf("./bam <inputFile> <outputFile.sam/bam>\n");
      exit(-1);
   }


   SamFile samIn;
      
   samIn.OpenForRead(argv[1]);

   SamFile samOut;

   samOut.OpenForWrite(argv[2]);

   // Read the sam header.
   SamFileHeader samHeader;
   samIn.ReadHeader(samHeader);

   samOut.WriteHeader(samHeader);

   // Read the first sam record.
   SamRecord samRecord;

   // Keep reading records until it fails.
   int recordCount = 0;
   while (samIn.ReadRecord(samHeader, samRecord) == true)
   {
      recordCount++;
      samOut.WriteRecord(samHeader, samRecord);
   }
   printf("RecordCount = %d\n", recordCount);
}