/// <summary>
/// Helper method for retrieving the number of reads with symbol at position.
/// </summary>
/// <param name="symbol">The symbol of interest</param>
/// <param name="position">Position in read sequence</param>
/// <returns>Number of reads</returns>
private int GetNumReadsAtPositionWithSymbol(byte symbol, int position)
{
int[] positions;
if (SymbolCountByPositionTable.TryGetValue(symbol, out positions))
{
return(positions[position]);
}
else
{
return(0);
}
}
/// <summary>
/// Iterate through each sequence and for each position, record the number of occurrences
/// of each base symbol
/// </summary>
public override void ContentByPosition()
{
if (this.Sequences == null)
{
throw new ArgumentNullException("Sequences");
}
foreach (var seqObj in this.Sequences)
{
if (Worker != null && WorkerArgs != null && Worker.CancellationPending)
{
WorkerArgs.Cancel = true;
break;
}
int p = 0;
// iterate through each position in sequence string
foreach (var symbol in seqObj)
{
int[] positions;
// check if SymbolCountByPositionTable has this symbol initialized
if (SymbolCountByPositionTable.TryGetValue(symbol, out positions))
{
positions[p]++;
SymbolCountByPositionTable[symbol] = positions;
}
else
{
// initialize a new List for this symbol
SymbolCountByPositionTable.Add(symbol, new int[this.ReadLengthMax]);
SymbolCountByPositionTable[symbol][p] = 1;
}
p++;
}
}
HasRunContentByPosition = true;
}