private bool setPositionsBasedOnAlignment(GenomeSlice slice)
{
Sequence s = new Sequence(DnaAlphabet.Instance, slice.Node.Sequence, false);
var delts = assemblyAligner.GetDeltaAlignments(s).SelectMany(x => x).ToList();
if (delts.Count > 0)
{
//check if reversed
if (delts[0].IsReverseQueryDirection)
{
slice.Node.ReversePath();
s = new Sequence(DnaAlphabet.Instance, slice.Node.Sequence, false);
delts = assemblyAligner.GetDeltaAlignments(s).SelectMany(x => x).ToList();
}
if (delts.Count == 1)
{
slice.SuggestedLeftSidePosition = delts[0].FirstSequenceStart;
slice.SuggestedRightSidePosition = delts[0].FirstSequenceEnd;
}
else if (delts.Count == 2) //split, happens in event of wrap around
{
slice.SuggestedLeftSidePosition = delts.MaxBy(x => x.FirstSequenceStart).FirstSequenceStart;
slice.SuggestedRightSidePosition = delts.MinBy(x => x.FirstSequenceEnd).FirstSequenceEnd;
}
else
{
return(false);
}
return(true);
}
return(false);
}
public static IEnumerable <IEnumerable <DeltaAlignment> > GetDeltaAlignments(ISequence querySequence)
{
return(nucmer.GetDeltaAlignments(querySequence));
}