/// <summary> /// Outputs the data for a FastqFile to the console, keeping code clean in other classes /// </summary> /// <param name="fqFile"></param> public void OutputFileDataToConsole(IFqFile fqFile) { Console.WriteLine("Joint Test Results Completed on " + fqFile.getTotalNucleotides() + " Nucleotides"); Console.WriteLine("Joint Test Results: " + fqFile.getGCount() + "G " + Math.Round(fqFile.gContents(), 2) + "% " + fqFile.getCCount() + "C " + Math.Round(fqFile.cContents(), 2) + " %"); Console.WriteLine("Misreads: " + fqFile.getNCount()); Console.WriteLine("Nucleotides Cleaned: {0}", fqFile.getNucleotidesCleaned()); Console.WriteLine("Distribution: " + fqFile.getDistribution().Count); Console.WriteLine("Stats Performed"); for (int i = 0; i < 20; i++) { FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i); Console.WriteLine("-- -Stats for Sequence " + (i + 1) + ": LB: {0} 1Q: {1} Median: {2} Mean: {3} 3Q: {4} UB: {5}", fqSeq.getLowerThreshold(), fqSeq.getFirstQuartile(), fqSeq.getMedian(), Math.Round(fqSeq.getMean(), 2), fqSeq.getThirdQuartile(), fqSeq.getUpperThreshold()); } for (int i = 0; i < fqFile.getDistribution().Count; i++) Console.WriteLine("---> Quality Score: {0} Count: {1}", i, fqFile.getDistribution()[i]); for (int i = 0; i < fqFile.GetPerBaseStatisticsArray().Length; i ++) Console.WriteLine("===> BaseStatistic: {0} \tCount: {1} LB: {2} 1Q: {3} Median: {4} Mean: {5} 3Q: {6} UB: {7}", i, fqFile.GetPerBaseStatisticsArray()[i].BaseCount, fqFile.GetPerBaseStatisticsArray()[i].LowerThreshold, fqFile.GetPerBaseStatisticsArray()[i].FirstQuartile, fqFile.GetPerBaseStatisticsArray()[i].Median, fqFile.GetPerBaseStatisticsArray()[i].Mean, fqFile.GetPerBaseStatisticsArray()[i].ThirdQuartile, fqFile.GetPerBaseStatisticsArray()[i].UpperThreshold); }
/// <summary> /// Outputs the data for a FastqFile to the console, keeping code clean in other classes /// </summary> /// <param name="fqFile"></param> public void OutputFileDataToConsole(IFqFile fqFile) { Console.WriteLine("Joint Test Results Completed on " + fqFile.getTotalNucleotides() + " Nucleotides"); Console.WriteLine("Joint Test Results: " + fqFile.getGCount() + "G " + Math.Round(fqFile.gContents(), 2) + "% " + fqFile.getCCount() + "C " + Math.Round(fqFile.cContents(), 2) + " %"); Console.WriteLine("Misreads: " + fqFile.getNCount()); Console.WriteLine("Nucleotides Cleaned: {0}", fqFile.getNucleotidesCleaned()); Console.WriteLine("Distribution: " + fqFile.getDistribution().Count); Console.WriteLine("Stats Performed"); for (int i = 0; i < 20; i++) { FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i); Console.WriteLine("-- -Stats for Sequence " + (i + 1) + ": LB: {0} 1Q: {1} Median: {2} Mean: {3} 3Q: {4} UB: {5}", fqSeq.getLowerThreshold(), fqSeq.getFirstQuartile(), fqSeq.getMedian(), Math.Round(fqSeq.getMean(), 2), fqSeq.getThirdQuartile(), fqSeq.getUpperThreshold()); } for (int i = 0; i < fqFile.getDistribution().Count; i++) { Console.WriteLine("---> Quality Score: {0} Count: {1}", i, fqFile.getDistribution()[i]); } for (int i = 0; i < fqFile.GetPerBaseStatisticsArray().Length; i++) { Console.WriteLine("===> BaseStatistic: {0} \tCount: {1} LB: {2} 1Q: {3} Median: {4} Mean: {5} 3Q: {6} UB: {7}", i, fqFile.GetPerBaseStatisticsArray()[i].BaseCount, fqFile.GetPerBaseStatisticsArray()[i].LowerThreshold, fqFile.GetPerBaseStatisticsArray()[i].FirstQuartile, fqFile.GetPerBaseStatisticsArray()[i].Median, fqFile.GetPerBaseStatisticsArray()[i].Mean, fqFile.GetPerBaseStatisticsArray()[i].ThirdQuartile, fqFile.GetPerBaseStatisticsArray()[i].UpperThreshold); } }
public void ContructComponentDetails(IFqFile component) { this.ComponentName = component.getFileName(); this.FileName = component.getFileName(); this.sequencerType = component.getSequencerType(); this.ComponentNumber = component.getComponentNumber(); this.TotalNucs = component.getTotalNucleotides(); this.TotalSequences = component.getFastqArraySize(); this.NucleotidesCleaned = component.getNucleotidesCleaned(); this.Distribution = component.getDistribution(); this.SequenceLengthDistribution = component.getSequenceLengthDistribution(); this.NCount = component.getNCount(); this.CCount = component.getCCount(); this.GCount = component.getGCount(); this.MaxSeqSize = component.getMaxSeqSize(); this.MinSeqSize = component.getMinSeqSize(); this.NPercent = component.nContents(); this.CPercent = component.cContents(); this.GPercent = component.gContents(); this.SequencesRemoved = component.getSequencesRemoved(); this.RemovedAdapters = component.getRemovedAdapters(); this.perBaseStatistics = component.GetPerBaseStatisticsArray(); }