/* * end point */ private void end(int endPoint) { int i = endPoint; stopwatch.Stop(); fastqFile.setSequencerType(sequencerType); if (fastqFile is FqFile_Component) { fastqFile.setFqHashMap(FastqController.getInstance().GetFqFileMap().ConstructSequencerSpecificReadMap(sequencerType)); Console.WriteLine("Calculating and setting sequencer specific file map to component"); } Console.WriteLine("Time To Determine ISequencer: " + stopwatch.Elapsed); Console.WriteLine("ISequencer Name: " + sequencerType); Console.WriteLine("File contains {0} sequences", fastqFile.getFastqArraySize()); }
private void sequencer(IFqFile fastqFile) { String sequencer = null; Boolean completed = false; Boolean sangerLowerBoundary = false, sangerUpperBoundary = false, solexaLowerBoundary = false, sharedUpperBoundary = false, illuminaThreeLowerBoundary = false, illuminaFiveLowerBoundary = false, illuminaEightLowerBoundary = false, illuminaNineLowerBoundary = false, illuminaEightNineUpperBoundary = false; // char variables for the upper and lower boundaries of the sequencer types char sangerLower = '!'; char sangerUpper = 'I'; char solexaLower = ';'; char solilmixedUpper = 'h'; char illuminathreeLower = '@'; char illuminafiveLower = 'B'; char illuminaeightLower = '!'; char illuminanineLower = '#'; char illuminamixedUpper = 'J'; Stopwatch stopwatch = new Stopwatch(); stopwatch.Start(); while (completed != true) { for (int i = 0; i < fastqFile.getFastqArraySize();i++) { FqSequence fqSeq = fastqFile.getFastqSequenceByPosition(i); for (int j = 0; j < fqSeq.getFastqSeqSize(); j++) { char qualityValue = map[fqSeq.getFastqSeqAtPosition(j)].getQualityRead(); if (qualityValue == sangerLower) sangerLowerBoundary = true; else if (qualityValue == sangerUpper) sangerUpperBoundary = true; else if (qualityValue == solexaLower) solexaLowerBoundary = true; else if (qualityValue == solilmixedUpper) sharedUpperBoundary = true; else if (qualityValue == illuminathreeLower)illuminaThreeLowerBoundary = true; else if (qualityValue == illuminafiveLower) illuminaFiveLowerBoundary = true; else if (qualityValue == illuminaeightLower)illuminaEightLowerBoundary = true; else if (qualityValue == illuminanineLower) illuminaNineLowerBoundary = true; else if (qualityValue == illuminamixedUpper)illuminaEightNineUpperBoundary = true; } } if (sangerLowerBoundary != false && sangerUpperBoundary != false && illuminaEightNineUpperBoundary != true) { sequencer = "Sanger"; completed = true; } else if (solexaLowerBoundary != false && sharedUpperBoundary != false) { sequencer = "Solexa"; completed = true; } else if (illuminaThreeLowerBoundary != false && sharedUpperBoundary != false && solexaLowerBoundary != true) { sequencer = "Illumina 1.3"; completed = true; } else if (illuminaFiveLowerBoundary != false && sharedUpperBoundary != false && illuminaThreeLowerBoundary != true) { sequencer = "Illumina 1.5"; completed = true; } else if (illuminaEightLowerBoundary != false && illuminaEightNineUpperBoundary != false) { sequencer = "Illumina 1.8"; completed = true; } else if (illuminaNineLowerBoundary != false && illuminaEightNineUpperBoundary != false && illuminaEightLowerBoundary != true) { sequencer = "Illumina 1.9"; completed = true; } else if (completed != true) { sequencer = "Default"; completed = true; } else if ((sequencer == null)) { sequencer = "Default"; completed = true; } } this.sequencerType = sequencer; fastqFile.setSequencerType(sequencerType); if (fastqFile is FqFile_Component) { fastqFile.setFqHashMap(FastqController.getInstance().GetFqFileMap().ConstructSequencerSpecificReadMap(sequencerType)); Console.WriteLine("Calculating and setting sequencer specific file map to component"); } stopwatch.Stop(); Console.WriteLine("Time To Determine ISequencer: " + stopwatch.Elapsed); Console.WriteLine("ISequencer Name: " + sequencer); Console.WriteLine("File contains {0} sequences", fastqFile.getFastqArraySize()); }
private void sequencer(IFqFile fastqFile) { String sequencer = null; Boolean completed = false; Boolean sangerLowerBoundary = false, sangerUpperBoundary = false, solexaLowerBoundary = false, sharedUpperBoundary = false, illuminaThreeLowerBoundary = false, illuminaFiveLowerBoundary = false, illuminaEightLowerBoundary = false, illuminaNineLowerBoundary = false, illuminaEightNineUpperBoundary = false; // char variables for the upper and lower boundaries of the sequencer types char sangerLower = '!'; char sangerUpper = 'I'; char solexaLower = ';'; char solilmixedUpper = 'h'; char illuminathreeLower = '@'; char illuminafiveLower = 'B'; char illuminaeightLower = '!'; char illuminanineLower = '#'; char illuminamixedUpper = 'J'; Stopwatch stopwatch = new Stopwatch(); stopwatch.Start(); while (completed != true) { for (int i = 0; i < fastqFile.getFastqArraySize(); i++) { FqSequence fqSeq = fastqFile.getFastqSequenceByPosition(i); for (int j = 0; j < fqSeq.getFastqSeqSize(); j++) { char qualityValue = map[fqSeq.getFastqSeqAtPosition(j)].getQualityRead(); if (qualityValue == sangerLower) { sangerLowerBoundary = true; } else if (qualityValue == sangerUpper) { sangerUpperBoundary = true; } else if (qualityValue == solexaLower) { solexaLowerBoundary = true; } else if (qualityValue == solilmixedUpper) { sharedUpperBoundary = true; } else if (qualityValue == illuminathreeLower) { illuminaThreeLowerBoundary = true; } else if (qualityValue == illuminafiveLower) { illuminaFiveLowerBoundary = true; } else if (qualityValue == illuminaeightLower) { illuminaEightLowerBoundary = true; } else if (qualityValue == illuminanineLower) { illuminaNineLowerBoundary = true; } else if (qualityValue == illuminamixedUpper) { illuminaEightNineUpperBoundary = true; } } } if (sangerLowerBoundary != false && sangerUpperBoundary != false && illuminaEightNineUpperBoundary != true) { sequencer = "Sanger"; completed = true; } else if (solexaLowerBoundary != false && sharedUpperBoundary != false) { sequencer = "Solexa"; completed = true; } else if (illuminaThreeLowerBoundary != false && sharedUpperBoundary != false && solexaLowerBoundary != true) { sequencer = "Illumina 1.3"; completed = true; } else if (illuminaFiveLowerBoundary != false && sharedUpperBoundary != false && illuminaThreeLowerBoundary != true) { sequencer = "Illumina 1.5"; completed = true; } else if (illuminaEightLowerBoundary != false && illuminaEightNineUpperBoundary != false) { sequencer = "Illumina 1.8"; completed = true; } else if (illuminaNineLowerBoundary != false && illuminaEightNineUpperBoundary != false && illuminaEightLowerBoundary != true) { sequencer = "Illumina 1.9"; completed = true; } else if (completed != true) { sequencer = "Default"; completed = true; } else if ((sequencer == null)) { sequencer = "Default"; completed = true; } } this.sequencerType = sequencer; fastqFile.setSequencerType(sequencerType); if (fastqFile is FqFile_Component) { fastqFile.setFqHashMap(FastqController.getInstance().GetFqFileMap().ConstructSequencerSpecificReadMap(sequencerType)); Console.WriteLine("Calculating and setting sequencer specific file map to component"); } stopwatch.Stop(); Console.WriteLine("Time To Determine ISequencer: " + stopwatch.Elapsed); Console.WriteLine("ISequencer Name: " + sequencer); Console.WriteLine("File contains {0} sequences", fastqFile.getFastqArraySize()); }