public override string GetAnnotation(Polymorphism poly)
{
int pos = poly.position;
string reference, alt, inBestHaplotype;
alt = "ERROR";
//TODO: Move this logic in to polymorphism class
if (poly.mutation == Mutations.INS)
{
reference = "-";
}
else
{
reference = Polymorphism.rCRS[poly.position - 1].ToString();
alt = poly.InsertedPolys;
}
if (poly.mutation == Mutations.DEL)
{
alt = "-";
}
else if (MutationAssigner.MutationIsBasePair(poly.mutation))
{
alt = MutationAssigner.getBase(poly.mutation);
}
if (!validPolys.ContainsKey(poly.position))
{
inBestHaplotype = "MutationExcludedFromSearch";
}
else
{
inBestHaplotype = bestMatch.MatchingPolymorphisms.Contains(poly).ToString();
}
return(String.Join(FIELD_DELIM, new[] { pos.ToString(), reference, alt, inBestHaplotype }));
}
public void AddPoly(Polymorphism p)
{
History.Add(p);
//This is a very backward way of representing this, as far as I can tell from the source code
//if 152C on the tree is followed by 152C!, then this means the 152C mutation should simply be cleared
if (p.isBackMutation)
{
//make sure we have one to remove
var toDrop = CurrentState.Where(x => x.position == p.position && x.mutation == p.mutation).ToList();
if (toDrop.Count != 1)
{
throw new HaploGrepException("Cannot back mutate when no mutation appeared!");
}
CurrentState.Remove(toDrop [0]);
}
else
{
var c1Count = CurrentState.Count == 1;
var c1SNP = MutationAssigner.MutationIsBasePair(CurrentState [0].mutation);
//simple SNP replacement
if (c1Count && c1SNP)
{
CurrentState.Clear();
CurrentState.Add(p);
}
//insertions are appended on, and once any deletion happens we are shit out of luck
else if (p.mutation == Mutations.INS && c1SNP && c1Count)
{
CurrentState.Add(p);
}
else if (p.mutation == Mutations.INS)
{
//Some spot have repeated inserts of the same base, e.g.
if (CurrentState.Any(z => z.mutation != Mutations.INS) || CurrentState.Any(z => z.InsertedPolys.Length > 1))
{
throw new HaploGrepException("Can't add insertions over multiple complex backgrounds");
}
else
{
//TODO: 455.1T and 455.2T are simply indicative of a two bp insertion (at the 1 position and the 2 position, this is totally confusiing).
//Verify that all insertions are the same, this happens in some cases such as 455.1T being followed by a 455.2T, note I know realize this
var set = new HashSet <string> (CurrentState.Select(x => x.insertedPolys));
set.Add(p.insertedPolys);
if (set.Count > 1)
{
throw new Exception("Cannot add a new type of insertion");
}
CurrentState.Add(p);
}
}
//Special exception for 1719.1G followed by 1719A, which is another odd case
else if (p.position == 1719 && p.ToString() == "1719A")
{
if (CurrentState.Count != 1 || CurrentState [0].ToString() != "1719.1G")
{
throw new HaploGrepException("1719 posiiton exception");
}
CurrentState.Add(p);
CurrentState.Reverse();
}
//this can happen if the base of interest is not the reference or last mutation.
else
{
if (!UnresolvedSeriesOfChanges.Contains(History))
{
UnresolvedSeriesOfChanges.Add(History);
}
throw new HaploGrepException("Tried to change a polymorphism at a location where a mutation already occurred without it being asimple thing!");
}
}
}