public IEnumerable <FastQ> ReadFastQ(string fileName)
{
int nLine = -1;
using (TextReader reader = File.OpenText(fileName))
{
string line;
while ((line = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0)
{
continue;
}
FastQ read = new FastQ()
{
Name = line,
Seq = reader.ReadLine(),
Comment = reader.ReadLine(),
Qual = reader.ReadLine()
};
nLine += 3;
yield return(read);
}
}
}
public void CountContexts(FastQ read)
{
for (int i = 0; i < read.Seq.Length - this.k; i++)
{
int currentCount = 0;
string kmer = read.Seq.Substring(i, this.k);
this.contextCounters.TryGetValue(kmer, out currentCount);
this.contextCounters[kmer] = currentCount + 1;
}
}