/// <summary>
/// Add alignment result and return the completed positions
/// </summary>
/// <param name="item">alignment result</param>
/// <returns>completed positions</returns>
public List<AlignedPositionMap> Add(SAMAlignedItem item)
{
List<AlignedPositionMap> result = null;
//if the alignment result moves to another chromosome, all uncompleted positions
//will be completed.
if (!item.Locations[0].Seqname.Equals(this.Chromosome))
{
result = Positions;
Positions = new List<AlignedPositionMap>();
PositionMap = new Dictionary<long, AlignedPositionMap>();
}
else if (this.Position != -1)
{
//if the alignment result position is larger than the last position in the uncompleted positions,
//all uncompleted positions will be completed.
if (item.Pos > this.Positions.Last().Position)
{
result = Positions;
Positions = new List<AlignedPositionMap>();
PositionMap = new Dictionary<long, AlignedPositionMap>();
}
else
{
//set up the completed list
result = new List<AlignedPositionMap>();
while (Positions[0].Position < item.Pos)
{
result.Add(Positions[0]);
PositionMap.Remove(Positions[0].Position);
Positions.RemoveAt(0);
}
}
}
List<AlignedPosition> align = item.GetAlignedPositions();
foreach (var asp in align)
{
AlignedPositionMap dic;
if (!PositionMap.TryGetValue(asp.Position, out dic))
{
dic = new AlignedPositionMap()
{
Chromosome = item.Locations[0].Seqname,
Position = asp.Position
};
Positions.Add(dic);
PositionMap[dic.Position] = dic;
}
List<AlignedPosition> curcount;
if (!dic.TryGetValue(asp.AlignedEvent, out curcount))
{
curcount = new List<AlignedPosition>();
dic[asp.AlignedEvent] = curcount;
}
curcount.Add(asp);
}
return result;
}
