/// <summary>
/// If duplicated adjacent tags are present, reduce them to one copy
/// </summary>
/// <returns>true if cigar was altered by compression</returns>
public bool Compress()
{
var newDirections = DirectionHelper.CompressDirections(Directions);
Directions = newDirections;
return(true);
}
private static string RecalculateApproximateStitchedDirections(CigarDirection cigarDirections, CigarAlignment cigarData, CigarAlignment newCigarData)
{
var cigarBaseDirectionMap = cigarDirections.Expand().ToArray();
var cigarBaseAlleleMap = cigarData.Expand();
var newCigarBaseAlleleMap = newCigarData.Expand();
var sequencedBaseDirectionMap = new DirectionType[cigarData.GetReadSpan()];
var directions = new List <DirectionOp>();
var sequencedBaseIndex = 0;
var cigarBaseIndex = 0;
var newCigarBaseIndex = 0;
while (true)
{
if (cigarBaseIndex >= cigarBaseAlleleMap.Count || newCigarBaseIndex >= newCigarBaseAlleleMap.Count)
{
// If new is longer than old, fill out the rest with the last direction of the old cigar
if (newCigarBaseIndex < newCigarBaseAlleleMap.Count)
{
directions.Add(new DirectionOp(cigarBaseDirectionMap[cigarBaseIndex - 1], newCigarBaseAlleleMap.Count - newCigarBaseIndex));
}
break;
}
while (!cigarBaseAlleleMap[cigarBaseIndex].IsReadSpan())
{
// Skip these
cigarBaseIndex++;
// TODO is it ever possible to go off the end here?
}
while (!newCigarBaseAlleleMap[newCigarBaseIndex].IsReadSpan())
{
directions.Add(new DirectionOp(cigarBaseDirectionMap[cigarBaseIndex], 1)); // TODO perhaps something more nuanced here? unclear what the best solution is. For now, just be consistent: take the last one that we were on at this point in the old cigar
newCigarBaseIndex++;
// TODO is it ever possible to go off the end here?
}
sequencedBaseDirectionMap[sequencedBaseIndex] = cigarBaseDirectionMap[cigarBaseIndex];
directions.Add(new DirectionOp(cigarBaseDirectionMap[cigarBaseIndex], 1));
sequencedBaseIndex++;
cigarBaseIndex++;
newCigarBaseIndex++;
}
var compressedDirections = DirectionHelper.CompressDirections(directions);
return(new CigarDirection(compressedDirections).ToString());
}
