public void Write(StreamWriter sw, FastqSequence seq)
{
sw.WriteLine("@" + seq.Reference);
sw.WriteLine(seq.SeqString);
sw.WriteLine(seq.Strand);
sw.WriteLine(seq.Score);
}
public void Write(StreamWriter sw, FastqSequence seq)
{
sw.WriteLine("@" + seq.Reference);
sw.WriteLine(seq.SeqString);
sw.WriteLine(seq.Strand);
sw.WriteLine(seq.Score);
}
/// <summary>
/// Gets the IEnumerable of FastqSequence from the stream being parsed.
/// </summary>
/// <param name="sr">Stream to be parsed.</param>
/// <returns>Returns a FastqSequence.</returns>
public FastqSequence Parse(TextReader sr)
{
while (true)
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (!String.IsNullOrWhiteSpace(line))
{
break;
}
}
if (line == null)
{
return(null);
}
if (!line.StartsWith("@"))
{
throw new Exception("Unrecognized line, should start with @ for query name: " + line);
}
var refer = line.Substring(1);
FastqSequence result = new FastqSequence(refer, null);
if (!AcceptName(result.Name))
{
sr.ReadLine();
sr.ReadLine();
sr.ReadLine();
Console.WriteLine("ignored " + result.Name);
continue;
}
result.SeqString = sr.ReadLine();
result.Strand = sr.ReadLine().StartsWith("-") ? '-' : '+';
result.Score = sr.ReadLine();
if (result.Score == null)
{
throw new Exception("Unrecognized line, cannot find score line of query: " + refer);
}
return(result);
}
}
/// <summary>
/// Gets the IEnumerable of FastqSequence from the stream being parsed.
/// </summary>
/// <param name="sr">Stream to be parsed.</param>
/// <returns>Returns a FastqSequence.</returns>
public FastqSequence Parse(TextReader sr)
{
while (true)
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (!String.IsNullOrWhiteSpace(line))
{
break;
}
}
if (line == null)
{
return null;
}
if (!line.StartsWith("@"))
{
throw new Exception("Unrecognized line, should start with @ for query name: " + line);
}
var refer = line.Substring(1);
FastqSequence result = new FastqSequence(refer, null);
if (!AcceptName(result.Name))
{
sr.ReadLine();
sr.ReadLine();
sr.ReadLine();
continue;
}
result.SeqString = sr.ReadLine();
result.Strand = sr.ReadLine().StartsWith("-") ? '-' : '+';
result.Score = sr.ReadLine();
if (result.Score == null)
{
throw new Exception("Unrecognized line, cannot find score line of query: " + refer);
}
return result;
}
}
