public override int CompareTo(Interval i2)
{
int comp = base.CompareTo(i2);
if (comp != 0)
{
return(comp);
}
Variant v2 = i2 as Variant;
if (v2 == null)
{
return(GetType().Name.CompareTo(i2.GetType().Name));
}
comp = ReferenceAlleleString.CompareTo(v2.ReferenceAlleleString);
if (comp != 0)
{
return(comp);
}
comp = SecondAlleleString.CompareTo(v2.SecondAlleleString);
if (comp != 0)
{
return(comp);
}
return(0);
}
public void CalculateType()
{
// Sanity check
if (SecondAlleleString.IndexOf(',') >= 0 || SecondAlleleString.IndexOf('/') >= 0)
{
throw new ArgumentException("Variants with multiple ALTs are not allowed (ALT: '" + SecondAlleleString + "')");
}
// Remove leading char (we still have some test cases using old TXT format)
if (ReferenceAlleleString == "*")
{
ReferenceAlleleString = "";
}
// Possibly some old formatting with +, -, and =
if (SecondAlleleString.StartsWith("+"))
{
// Insertion
SecondAlleleString = ReferenceAlleleString + SecondAlleleString.Substring(1);
}
else if (SecondAlleleString.StartsWith("-"))
{
// Deletion
ReferenceAlleleString = SecondAlleleString.Substring(1);
SecondAlleleString = "";
}
else if (SecondAlleleString.StartsWith("="))
{
// Mixed variant
SecondAlleleString = SecondAlleleString.Substring(1);
}
//---
// Calculate variant type
//---
if (ReferenceAlleleString == SecondAlleleString)
{
VarType = VariantType.INTERVAL;
}
else if (ReferenceAlleleString.Length == 1 && SecondAlleleString.Length == 1)
{
VarType = VariantType.SNV;
}
else if (ReferenceAlleleString.Length == SecondAlleleString.Length)
{
VarType = VariantType.MNV;
}
else if (ReferenceAlleleString.Length < SecondAlleleString.Length && SecondAlleleString.StartsWith(ReferenceAlleleString))
{
VarType = VariantType.INS;
}
else if (ReferenceAlleleString.Length > SecondAlleleString.Length && ReferenceAlleleString.StartsWith(SecondAlleleString))
{
VarType = VariantType.DEL;
}
else
{
VarType = VariantType.MIXED;
}
//---
// Start and end position
// - Start is always the leftmost base
// - End is always the rightmost affected base in the ReferenceAlleleStringerence genome
//---
if (VarType == VariantType.INS || VarType == VariantType.SNV)
{
// These changes only affect one position in the reference genome
OneBasedEnd = OneBasedStart;
}
else // if (isDel() || isMnp()) {
{
// Update 'end' position
if (ReferenceAlleleString.Length > 1)
{
OneBasedEnd = OneBasedStart + ReferenceAlleleString.Length - 1;
}
}
}