public void write(BamWriter writer,
int index)
{
SerializedBamAlignment alignment = _bamAlignmentList[index];
byte[] byteArray = null;
int smallOffset = 0;
_serializedAlignments.GetByteArrayAndOffset(alignment.SerializedOffset, ref byteArray, ref smallOffset);
writer.Write(byteArray, (uint)alignment.SerializedSize, smallOffset);
}
public override void WriteCurrentAlignment(BamWriter writer)
{
byte[] serializedAlignment = BamWriter.SerializeAlignment(ref _currentBamAlignment);
writer.Write(serializedAlignment, (uint)serializedAlignment.Length);
}