public void Reset()
{
R1Ops?.Clear();
R2Ops?.Clear();
R1OpsCount = 0;
R2OpsCount = 0;
}
public void Reset()
{
R1Ops?.Clear();
R2Ops?.Clear();
R1OpsCount = 0;
R2OpsCount = 0;
R1HasReferenceSpan = false;
R2HasReferenceSpan = false;
}
public void AddOpsForRead(ReadNumber num, List <CigarOp> ops)
{
if (num == ReadNumber.Read1)
{
R1Ops.AddRange(ops);
}
else
{
R2Ops.AddRange(ops);
}
}
public void AddOpsForRead(ReadNumber num, StitchableItem ops)
{
if (num == ReadNumber.Read1)
{
R1OpsCount++;
R1Ops.Add(ops);
}
else
{
R2OpsCount++;
R2Ops.Add(ops);
}
}
public void AddOpsForRead(ReadNumber num, List <StitchableItem> ops)
{
if (num == ReadNumber.Read1)
{
R1OpsCount += ops.Count;
R1Ops.AddRange(ops);
}
else
{
R2OpsCount += ops.Count;
R2Ops.AddRange(ops);
}
}
public void AddOpsForRead(ReadNumber num, List <StitchableItem> ops)
{
if (num == ReadNumber.Read1)
{
R1OpsCount += ops.Count;
R1Ops.AddRange(ops);
if (!R1HasReferenceSpan)
{
R1HasReferenceSpan = ops.Any(x => CigarExtensions.IsReferenceSpan(x.CigarOp));
}
}
else
{
R2OpsCount += ops.Count;
R2Ops.AddRange(ops);
if (!R2HasReferenceSpan)
{
R2HasReferenceSpan = ops.Any(x => CigarExtensions.IsReferenceSpan(x.CigarOp));
}
}
}
public void AddOpsForRead(ReadNumber num, StitchableItem ops)
{
if (num == ReadNumber.Read1)
{
R1OpsCount++;
R1Ops.Add(ops);
if (CigarExtensions.IsReferenceSpan(ops.CigarOp))
{
R1HasReferenceSpan = true;
}
}
else
{
R2OpsCount++;
R2Ops.Add(ops);
if (CigarExtensions.IsReferenceSpan(ops.CigarOp))
{
R2HasReferenceSpan = true;
}
}
}
public bool R1HasInsertion()
{
return(R1Ops != null && R1Ops.Any(x => x.CigarOp == 'I'));
}
public string Stringify()
{
return(string.Join("", R1Ops?.Select(x => x.CigarOp)) + "/" +
string.Join("", R2Ops?.Select(x => x.CigarOp)));
}
public bool R1HasInsertion()
{
return(R1Ops.Any(x => x.Type == 'I'));
}
public void Reset()
{
R1Ops.Clear();
R2Ops.Clear();
}
public string Stringify()
{
return(string.Join("", R1Ops.Select(x => x?.Type)) + "/" +
string.Join("", R2Ops.Select(x => x?.Type)));
}