public int CompareTo(object other)
{
CovPoint oth = (CovPoint)other;
int res = Point.CompareTo(oth.Point);
if (res == 0)
{
if (this.IsStart == oth.IsStart)
{
return(0);
}
else if (IsStart)
{
return(-1);
}
else
{
return(1);
}
}
return(res);
}
public virtual double GetCoverageSection(int st, int ed)
{
if (Reads != null)
{
int len = ed - st + 1;
List <CovPoint> points = new List <CovPoint> ();
List <CovPoint> remPoints = new List <CovPoint> ();
CovPoint OldEnd;
bool previousWasStart = false;
foreach (SeqRead sq in Reads)
{
if (HasOverLap(sq, st, ed))
{
foreach (CovPoint co in points)
{
if (sq.Contains(co.Point))
{
remPoints.Add(co);
}
}
foreach (CovPoint co in remPoints)
{
points.Remove(co);
}
remPoints.Clear();
if (sq.Start < st)
{
points.Add(new CovPoint(st, true));
}
else
{
points.Add(new CovPoint(sq.Start, true));
}
if (sq.End > ed)
{
points.Add(new CovPoint(ed, false));
}
else
{
points.Add(new CovPoint(sq.End, false));
}
points.Sort();
previousWasStart = false;
OldEnd = null;
foreach (CovPoint co in points)
{
if (co.IsStart)
{
if (previousWasStart)
{
remPoints.Add(co);
}
}
else
{
if (!previousWasStart)
{
remPoints.Add(OldEnd);
}
}
OldEnd = co;
previousWasStart = co.IsStart;
}
foreach (CovPoint c in remPoints)
{
points.Remove(c);
}
remPoints.Clear();
}
}
int totalGap = 0;
int lInd = points.Count - 1;
if (lInd > 0)
{
if (points [0].IsStart)
{
totalGap += points [0].Point - st;
}
if (!points [lInd].IsStart)
{
totalGap += ed - points [lInd].Point;
}
}
else
{
totalGap = len;
}
if (lInd > 1)
{
CovPoint previous = null;
previousWasStart = true;
foreach (CovPoint co in points)
{
if (previous != null)
{
if (co.IsStart && !previousWasStart)
{
totalGap += co.Point - previous.Point;
}
}
previous = co;
previousWasStart = co.IsStart;
}
}
return(1 - totalGap / (double)len);
}
else
{
return(0);
}
}
