protected void LoadKnownCN(string oracleVCFPath)
{
// Load our "oracle" of known copy numbers:
this.KnownCN = new Dictionary <string, List <CNInterval> >();
int count = 0;
using (FileStream stream = new FileStream(oracleVCFPath, FileMode.Open, FileAccess.Read))
using (StreamReader reader = new StreamReader(stream))
{
while (true)
{
string fileLine = reader.ReadLine();
if (fileLine == null)
{
break;
}
if (fileLine.Length == 0 || fileLine[0] == '#')
{
continue;
}
string[] bits = fileLine.Split('\t');
string chromosome = bits[0];
if (!KnownCN.ContainsKey(chromosome))
{
KnownCN[chromosome] = new List <CNInterval>();
}
CNInterval interval = new CNInterval();
interval.Start = int.Parse(bits[1]);
interval.CN = -1;
bits = bits[7].Split(';');
foreach (string subBit in bits)
{
if (subBit.StartsWith("CN="))
{
interval.CN = int.Parse(subBit.Substring(3));
}
if (subBit.StartsWith("END="))
{
interval.End = int.Parse(subBit.Substring(4));
}
}
if (interval.End == 0 || interval.CN < 0)
{
Console.WriteLine("Error - bogus record!");
Console.WriteLine(fileLine);
}
else
{
KnownCN[chromosome].Add(interval);
count++;
}
}
}
Console.WriteLine(">>>Loaded {0} known-CN intervals", count);
}
protected void LoadKnownCN(string oracleVCFPath)
{
// Load our "oracle" of known copy numbers:
this.KnownCN = new Dictionary<string, List<CNInterval>>();
int count = 0;
using (StreamReader reader = new StreamReader(oracleVCFPath))
{
while (true)
{
string fileLine = reader.ReadLine();
if (fileLine == null) break;
if (fileLine.Length == 0 || fileLine[0] == '#') continue;
string[] bits = fileLine.Split('\t');
string chromosome = bits[0];
if (!KnownCN.ContainsKey(chromosome)) KnownCN[chromosome] = new List<CNInterval>();
CNInterval interval = new CNInterval();
interval.Start = int.Parse(bits[1]);
interval.CN = -1;
bits = bits[7].Split(';');
foreach (string subBit in bits)
{
if (subBit.StartsWith("CN="))
{
interval.CN = int.Parse(subBit.Substring(3));
}
if (subBit.StartsWith("END="))
{
interval.End = int.Parse(subBit.Substring(4));
}
}
if (interval.End == 0 || interval.CN < 0)
{
Console.WriteLine("Error - bogus record!");
Console.WriteLine(fileLine);
}
else
{
KnownCN[chromosome].Add(interval);
count++;
}
}
}
Console.WriteLine(">>>Loaded {0} known-CN intervals", count);
}
