public override bool PrepareOptions()
{
var files = FastqFiles.TakeWhile(m => !File.Exists(m)).ToList();
if (files.Count > 0)
{
ParsingErrors.Add(string.Format("Thoese files not exists {0}.", files.Merge("\n")));
return false;
}
var gzipfile = new GzipTextReader(null);
if (FastqFiles.Any(m => gzipfile.NeedProcess(m)))
{
if (!File.Exists(this.Gzip))
{
ParsingErrors.Add(string.Format("Gzip not exists {0}.", this.Gzip));
return false;
}
}
if (FastqFiles.Count != OutputFiles.Count)
{
ParsingErrors.Add(string.Format("Count of FastQ not exists {0}.", this.Gzip));
return false;
}
return true;
}
public override bool PrepareOptions()
{
var files = FastqFiles.TakeWhile(m => !File.Exists(m)).ToList();
if (files.Count > 0)
{
ParsingErrors.Add(string.Format("Thoese files not exists {0}.", files.Merge("\n")));
return(false);
}
var gzipfile = new GzipTextReader(null);
if (FastqFiles.Any(m => gzipfile.NeedProcess(m)))
{
if (!File.Exists(this.Gzip))
{
ParsingErrors.Add(string.Format("Gzip not exists {0}.", this.Gzip));
return(false);
}
}
if (FastqFiles.Count != OutputFiles.Count)
{
ParsingErrors.Add(string.Format("Count of FastQ not exists {0}.", this.Gzip));
return(false);
}
return(true);
}
public override IEnumerable <string> Process(string fileName)
{
IFilter <FastqSequence> filter = options.GetFilter();
using (GzipTextReader gz1 = new GzipTextReader(options.Gzip, options.FastqFiles[0]))
using (GzipTextReader gz2 = new GzipTextReader(options.Gzip, options.FastqFiles[1]))
using (StreamWriter sw1 = new StreamWriter(options.OutputFiles[0]))
using (StreamWriter sw2 = new StreamWriter(options.OutputFiles[1]))
{
FastqReader reader = new FastqReader();
FastqWriter writer = new FastqWriter();
var count = 0;
while (true)
{
var q1 = reader.Parse(gz1.Reader);
var q2 = reader.Parse(gz2.Reader);
if (q1 == null || q2 == null)
{
break;
}
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (filter.Accept(q1) && filter.Accept(q2))
{
writer.Write(sw1, q1);
writer.Write(sw2, q2);
}
}
}
return(options.OutputFiles);
}
public override IEnumerable<string> Process(string fileName)
{
IFilter<FastqSequence> filter = options.GetFilter();
using (GzipTextReader gz1 = new GzipTextReader(options.Gzip, options.FastqFiles[0]))
using (GzipTextReader gz2 = new GzipTextReader(options.Gzip, options.FastqFiles[1]))
using (StreamWriter sw1 = new StreamWriter(options.OutputFiles[0]))
using (StreamWriter sw2 = new StreamWriter(options.OutputFiles[1]))
{
FastqReader reader = new FastqReader();
FastqWriter writer = new FastqWriter();
var count = 0;
while (true)
{
var q1 = reader.Parse(gz1.Reader);
var q2 = reader.Parse(gz2.Reader);
if (q1 == null || q2 == null)
{
break;
}
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (filter.Accept(q1) && filter.Accept(q2))
{
writer.Write(sw1, q1);
writer.Write(sw2, q2);
}
}
}
return options.OutputFiles;
}
