public override IEnumerable<string> Process()
{
Progress.SetMessage("This pair end bam file has been sorted by name, it will cost less time to generate fastq files ...");
var output1 = _options.OutputPrefix + ".1.fastq";
var output2 = _options.OutputPrefix + ".2.fastq";
if (!_options.UnGzipped)
{
output1 = output1 + ".gz";
output2 = output2 + ".gz";
}
var tmp1 = output1 + ".tmp";
var tmp2 = output2 + ".tmp";
var output3 = Path.ChangeExtension(_options.OutputPrefix, ".orphan.fastq");
var paired = new FastqItem[3];
string lastname = null;
using (var sw1 = StreamUtils.GetWriter(tmp1, !_options.UnGzipped))
{
using (var sw2 = StreamUtils.GetWriter(tmp2, !_options.UnGzipped))
{
using (var sw3 = new StreamWriter(output3))
{
var sw = new[] { null, sw1, sw2, sw3 };
using (var sr = new FastqItemBAMParser(_options.InputFile))
{
FastqItem ss;
var count = 0;
var outputCount = 0;
while ((ss = sr.ParseNext()) != null)
{
if (string.IsNullOrEmpty(ss.Qname))
{
throw new Exception(string.Format("Entry after {0} has empty name", lastname));
}
ss.CheckPairedName();
if (string.IsNullOrEmpty(ss.Qname))
{
throw new Exception(string.Format("After check paired name, entry after {0} has empty name", lastname));
}
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads processed.", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (lastname == null)
{
paired[ss.PairIndex] = ss;
lastname = ss.PairName;
continue;
}
if (ss.PairName.Equals(lastname))
{
paired[ss.PairIndex] = ss;
continue;
}
outputCount = WriteFastq(paired, sw, outputCount);
paired[1] = null;
paired[2] = null;
paired[ss.PairIndex] = ss;
lastname = ss.PairName;
}
WriteFastq(paired, sw, outputCount);
}
}
}
}
if (File.Exists(output1))
{
File.Delete(output1);
}
File.Move(tmp1, output1);
if (File.Exists(output2))
{
File.Delete(output2);
}
File.Move(tmp2, output2);
if (new FileInfo(output3).Length == 0)
{
File.Delete(output3);
}
return new[] { output1, output2 };
}
public override IEnumerable <string> Process()
{
Progress.SetMessage("This pair end bam file has been sorted by name, it will cost less time to generate fastq files ...");
var output1 = _options.OutputPrefix + ".1.fastq";
var output2 = _options.OutputPrefix + ".2.fastq";
if (!_options.UnGzipped)
{
output1 = output1 + ".gz";
output2 = output2 + ".gz";
}
var tmp1 = output1 + ".tmp";
var tmp2 = output2 + ".tmp";
var output3 = Path.ChangeExtension(_options.OutputPrefix, ".orphan.fastq");
var paired = new FastqItem[3];
string lastname = null;
using (var sw1 = StreamUtils.GetWriter(tmp1, !_options.UnGzipped))
{
using (var sw2 = StreamUtils.GetWriter(tmp2, !_options.UnGzipped))
{
using (var sw3 = new StreamWriter(output3))
{
var sw = new[] { null, sw1, sw2, sw3 };
using (var sr = new FastqItemBAMParser(_options.InputFile))
{
FastqItem ss;
var count = 0;
var outputCount = 0;
while ((ss = sr.ParseNext()) != null)
{
if (string.IsNullOrEmpty(ss.Qname))
{
throw new Exception(string.Format("Entry after {0} has empty name", lastname));
}
ss.CheckPairedName();
if (string.IsNullOrEmpty(ss.Qname))
{
throw new Exception(string.Format("After check paired name, entry after {0} has empty name", lastname));
}
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads processed.", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (lastname == null)
{
paired[ss.PairIndex] = ss;
lastname = ss.PairName;
continue;
}
if (ss.PairName.Equals(lastname))
{
paired[ss.PairIndex] = ss;
continue;
}
outputCount = WriteFastq(paired, sw, outputCount);
paired[1] = null;
paired[2] = null;
paired[ss.PairIndex] = ss;
lastname = ss.PairName;
}
WriteFastq(paired, sw, outputCount);
}
}
}
}
if (File.Exists(output1))
{
File.Delete(output1);
}
File.Move(tmp1, output1);
if (File.Exists(output2))
{
File.Delete(output2);
}
File.Move(tmp2, output2);
if (new FileInfo(output3).Length == 0)
{
File.Delete(output3);
}
return(new[] { output1, output2 });
}
private int WriteFastq(FastqItem[] paired, StreamWriter[] sw, int outputCount)
{
if (paired[1] != null && paired[2] != null)
{
paired[1].WriteFastq(sw[1]);
paired[2].WriteFastq(sw[2]);
outputCount++;
if (outputCount % 1000000 == 0)
{
GC.Collect();
GC.WaitForPendingFinalizers();
Progress.SetMessage(string.Format("{0} paired reads processed, cost memory: {1} MB", outputCount, (GC.GetTotalMemory(true) / 1048576)));
}
}
else if (paired[1] != null)
{
paired[1].WriteFastq(sw[3]);
}
else
{
paired[2].WriteFastq(sw[3]);
}
return outputCount;
}
