public void Compress()
{
var directionString = "1F2S1S1R";
var directions = new CigarDirection(directionString);
var uncompressedDirections = new List <DirectionOp>()
{
GetDirectionOp(DirectionType.Forward, 1),
GetDirectionOp(DirectionType.Stitched, 2),
GetDirectionOp(DirectionType.Stitched, 1),
GetDirectionOp(DirectionType.Reverse, 1),
};
Assert.Equal(directionString, directions.ToString());
CompareDirections(uncompressedDirections, directions.Directions);
directions.Compress();
var compressedDirections = new List <DirectionOp>()
{
GetDirectionOp(DirectionType.Forward, 1),
GetDirectionOp(DirectionType.Stitched, 3),
GetDirectionOp(DirectionType.Reverse, 1),
};
CompareDirections(compressedDirections, directions.Directions);
}
public StitchingInfo()
{
StitchedCigar = new CigarAlignment();
StitchedDirections = new CigarDirection();
StitchedBases = new List <char>();
StitchedQualities = new List <byte>();
}
private List <string> ExpandCigar(CigarAlignment cigar, CigarDirection directions)
{
var expandedDirections = new List <DirectionType>();
foreach (var direction in directions.Directions)
{
for (var i = 0; i < direction.Length; i++)
{
expandedDirections.Add(direction.Direction);
}
}
var expandedCigar = new List <string>();
var index = 0;
foreach (CigarOp op in cigar)
{
for (var i = 0; i < op.Length; i++)
{
expandedCigar.Add(op.Type.ToString()[0].ToString());
}
}
var expandedCigarDirection = new List <string>();
for (int i = 0; i < expandedCigar.Count; i++)
{
var cigarChunk = expandedCigar[i].ToString() + expandedDirections[i].ToString()[0];
expandedCigarDirection.Add(cigarChunk);
}
return(expandedCigarDirection);
}
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());
}
public void Expander()
{
var directionString = "2F3S2R";
var directions = new CigarDirection(directionString);
var expandedDirections = directions.Expand();
int i = 0;
for (var expander = new CigarDirectionExpander(directions); expander.IsNotEnd(); expander.MoveNext())
{
Assert.Equal(expandedDirections[i], expander.Current);
++i;
}
}
public void Constructor()
{
var directionString = "1F2S1R";
var expectedDirections = new List <DirectionOp>()
{
GetDirectionOp(DirectionType.Forward, 1),
GetDirectionOp(DirectionType.Stitched, 2),
GetDirectionOp(DirectionType.Reverse, 1),
};
var cigarDirection = new CigarDirection(directionString);
Assert.Equal(directionString, cigarDirection.ToString());
CompareDirections(expectedDirections, cigarDirection.Directions);
}
public void Expand()
{
var directionString = "2F3S2R";
var directions = new CigarDirection(directionString);
var expandedDirections = new List <DirectionType>()
{
DirectionType.Forward,
DirectionType.Forward,
DirectionType.Stitched,
DirectionType.Stitched,
DirectionType.Stitched,
DirectionType.Reverse,
DirectionType.Reverse
};
CompareDirectionTypes(expandedDirections, directions.Expand());
}
public static string GetUpdatedXdForRealignedStitchedRead(BamAlignment origRead, BamAlignment realignedRead)
{
var origXdString = origRead.GetStringTag("XD");
if (origXdString == null)
{
// If we're properly only doing this on stuff that was already stitched, this should never happen anyway
return(null);
}
if (ReadContainsDeletions(origRead) || ReadContainsDeletions(realignedRead))
{
var origXd = new CigarDirection(origXdString);
var newXd = RecalculateApproximateStitchedDirections(origXd, origRead.CigarData, realignedRead.CigarData);
return(newXd);
}
else
{
// We can keep the orig cigar directions - length hasn't changed
return(origXdString);
}
}
public StitchingInfo()
{
StitchedCigar = new CigarAlignment();
StitchedDirections = new CigarDirection();
}
