public Read DeepCopy()
{
var read = new Read(Chromosome, new BamAlignment(BamAlignment));
if (_stitchedCigarInitialized)
{
read.StitchedCigar = StitchedCigar.DeepCopy();
}
//read.StitchedCigar = StitchedCigar; // copy this one - it may have been reset
if (_directionCigarInitialized)
{
read.CigarDirections = new CigarDirection(CigarDirections.ToString());
}
if (_sequencedBaseDirectionMapInitialized)
{
read.SequencedBaseDirectionMap = (DirectionType[])SequencedBaseDirectionMap.Clone();
}
if (_positionMapInitialized)
{
read.PositionMap = (int[])PositionMap.Clone();
}
return(read);
}
private void SetSequencedBaseDirectionMapFromBam()
{
try
{
if (_sequencedBaseDirectionMap == null || _sequencedBaseDirectionMap.Length != ReadLength)
{
_sequencedBaseDirectionMap = new DirectionType[ReadLength];
if (CigarDirections != null && (CigarDirections.Directions.Count > 0))
{
_expandedBaseDirectionMap = CigarDirections.Expand().ToArray();
_sequencedBaseDirectionMap = CreateSequencedBaseDirectionMap(_expandedBaseDirectionMap, CigarData);
}
else
{
var reverse = BamAlignment.IsReverseStrand();
for (var i = 0; i < ReadLength; i++)
{
_sequencedBaseDirectionMap[i] = reverse ? DirectionType.Reverse : DirectionType.Forward;
}
}
_sequencedBaseDirectionMapInitialized = true;
}
}
catch (Exception e)
{
throw new Exception("Exception caught in " + Name + ": " + e.StackTrace, e);
}
}
