/// <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();
}
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();
}
