public CigarAlignment DeepCopy()
{
CigarAlignment val = new CigarAlignment();
foreach (CigarOp op in _data)
{
val.Add(op.DeepCopy());
}
return(val);
}
/// <summary>
/// Copy constructor.
/// </summary>
public BamAlignment(BamAlignment a)
{
AlignmentFlag = a.AlignmentFlag;
Bases = a.Bases;
Bin = a.Bin;
CigarData = new CigarAlignment(a.CigarData.ToString());
FragmentLength = a.FragmentLength;
MapQuality = a.MapQuality;
MatePosition = a.MatePosition;
MateRefID = a.MateRefID;
Name = a.Name;
Position = a.Position;
Qualities = new byte[a.Qualities.Length];
Array.Copy(a.Qualities, Qualities, Qualities.Length);
RefID = a.RefID;
TagData = a.TagData;
_endPosition = a._endPosition;
}
/// <summary>
/// constructor
/// </summary>
public BamAlignment()
{
//tjd+
//
//This is a deliberate departure from the Isas lib (which leaves these two values unset)
//When this is set to 0 (by simply being left unset)
//that is a real index value. So trouble can occur wehn unmapped reads might appear to have a mate at ChrM.
//How best to refactor this is currently under discussion with the Isas team.
//
//Related PISCES pull request:
//(see BamAlignment constructor in BamCommon.cs):
//https://git.illumina.com/Bioinformatics/Pisces5/pull/495/files
//Related ISAS pull request:
//https://git.illumina.com/Isas/SequencingFiles/pull/127
//
//tjd-
MatePosition = -1;
MateRefID = -1;
//tjd-
CigarData = new CigarAlignment();
_endPosition = null;
}
public CigarAlignment(CigarAlignment other)
{
_data = new List <CigarOp>(other._data);
}
public byte[] TagData; // Tag data (accessors will pull the requested information out)
// constructor
public BamAlignment()
{
MatePosition = -1;
MateRefID = -1;
CigarData = new CigarAlignment();
}