// writes an alignment
public void WriteAlignment(BamAlignment al)
{
if (!IsOpen)
{
throw new IOException(string.Format("ERROR: Tried to write an alignment but the file has not been opened yet."));
}
// initialize
uint nameLen = (uint)al.Name.Length + 1;
uint numBases = (uint)al.Bases.Length;
uint numCigarOperations = (uint)al.CigarData.Count;
uint packedCigarLen = numCigarOperations * 4;
uint numEncodedBases = (uint)((numBases / 2.0) + 0.5);
uint tagDataLen = (uint)al.TagData.Length;
uint dataBlockSize = nameLen + packedCigarLen + numEncodedBases + numBases + tagDataLen;
uint alignBlockSize = BamConstants.CoreAlignmentDataLen + dataBlockSize;
uint blockSize = alignBlockSize + 4;
int offset = 0;
// test if we should flush the block
if ((BlockOffset + blockSize) > MaxBlockSize)
{
FlushBlock();
}
// redimension the buffer if needed
if (blockSize > _outputBuffer.Length)
{
_outputBuffer = new byte[blockSize + 1024];
}
// store the block size
BinaryIO.AddUIntBytes(ref _outputBuffer, ref offset, alignBlockSize);
// store the BAM core data
BinaryIO.AddIntBytes(ref _outputBuffer, ref offset, al.RefID);
BinaryIO.AddIntBytes(ref _outputBuffer, ref offset, al.Position);
BinaryIO.AddUIntBytes(ref _outputBuffer, ref offset, (al.Bin << 16) | (al.MapQuality << 8) | nameLen);
BinaryIO.AddUIntBytes(ref _outputBuffer, ref offset, (al.AlignmentFlag << 16) | numCigarOperations);
BinaryIO.AddUIntBytes(ref _outputBuffer, ref offset, numBases);
BinaryIO.AddIntBytes(ref _outputBuffer, ref offset, al.MateRefID);
BinaryIO.AddIntBytes(ref _outputBuffer, ref offset, al.MatePosition);
BinaryIO.AddIntBytes(ref _outputBuffer, ref offset, al.FragmentLength);
// store the alignment name
BinaryIO.AddNullTerminatedString(ref _outputBuffer, ref offset, al.Name);
// store the packed CIGAR string and packed bases
PackCigar(ref offset, ref _outputBuffer, al.CigarData);
PackBases(ref offset, numEncodedBases, al.Bases);
// store the base qualities
Buffer.BlockCopy(al.Qualities, 0, _outputBuffer, offset, al.Qualities.Length);
offset += al.Qualities.Length;
// store the tag data
Buffer.BlockCopy(al.TagData, 0, _outputBuffer, offset, al.TagData.Length);
offset += al.TagData.Length;
// write the alignment
Write(_outputBuffer, blockSize);
}
