public void AddBaseQualites(int position, AlleleType alleleType, DirectionType directionType, double baseQuality, int anchorType)
{
if (IsPositionInRegion(position))
{
_sumOfAlleleBaseQualities[position - StartPosition, (int)alleleType, (int)directionType, anchorType] += baseQuality;
}
}
public void AddAlleleCount(int position, AlleleType alleleType, DirectionType directionType, int anchorType)
{
if (IsPositionInRegion(position))
{
_alleleCounts[position - StartPosition, (int)alleleType, (int)directionType, anchorType]++;
}
}
public double GetSumOfAlleleBaseQualites(int position, AlleleType alleleType, DirectionType directionType)
{
if (!IsPositionInRegion(position))
{
throw new ArgumentException(string.Format("Position {0} is not in region '{1}'.", position, Name));
}
return(_sumOfAlleleBaseQualities[position - StartPosition, (int)alleleType, (int)directionType]);
}
public int GetAlleleCount(int position, AlleleType alleleType, DirectionType directionType)
{
if (!IsPositionInRegion(position))
{
throw new ArgumentException(string.Format("Position {0} is not in region '{1}'.", position, Name));
}
return(_alleleCounts[position - StartPosition, (int)alleleType, (int)directionType]);
}
public double GetSumOfAlleleBaseQualites(int position, AlleleType alleleType, DirectionType directionType, int minAnchor = 0, int?maxAnchor = null, bool fromEnd = false, bool symmetric = false)
{
if (!IsPositionInRegion(position))
{
throw new ArgumentException(string.Format("Position {0} is not in region '{1}'.", position, Name));
}
var totCount = AlleleCountHelper.GetAnchorAdjustedTotalQuality(minAnchor, fromEnd, WellAnchoredIndex, NumAnchorIndexes,
_sumOfAlleleBaseQualities, position - StartPosition, (int)alleleType, (int)directionType, _numAnchorTypes, maxAnchor, symmetric);
return(totCount);
}
public double GetSumOfAlleleBaseQualities(int position, AlleleType alleleType, DirectionType directionType, int minAnchor = 0, int?maxAnchor = null, bool fromEnd = false, bool symmetric = false)
{
var region = GetBlock(position, false);
return(region == null ? 0 : region.GetSumOfAlleleBaseQualites(position, alleleType, directionType, minAnchor, maxAnchor, fromEnd));
}
private void AddAlleleBaseQuality(int position, AlleleType alleleType, DirectionType directionType, double baseQuality, int anchorType)
{
var block = GetBlock(position);
block.AddBaseQualites(position, alleleType, directionType, baseQuality, anchorType);
}
private void AddAlleleCount(int position, AlleleType alleleType, DirectionType directionType, int anchorType)
{
var block = GetBlock(position);
block.AddAlleleCount(position, alleleType, directionType, anchorType);
}
public int GetAlleleCount(int position, AlleleType alleleType, DirectionType directionType, int minAnchor = 0, int?maxAnchor = null, bool fromEnd = false, bool symmetric = false)
{
var region = GetBlock(position, false);
return(region == null ? 0 : region.GetAlleleCount(position, alleleType, directionType, minAnchor, maxAnchor, fromEnd, symmetric));
}
public int GetAlleleCount(int position, AlleleType alleleType, DirectionType directionType)
{
var region = GetBlock(position, false);
return(region == null ? 0 : region.GetAlleleCount(position, alleleType, directionType));
}
public AlleleCount(AlleleType alleleType)
{
AlleleType = alleleType;
}
public double GetSumOfAlleleBaseQualities(int position, AlleleType alleleType, DirectionType directionType)
{
var region = GetBlock(position, false);
return(region?.GetSumOfAlleleBaseQualites(position, alleleType, directionType) ?? 0);
}
