/**
* This method outlines the first decision to test quality data and return whether it resides
* in the higher ASCII regions greater than character J or in the lower regions below this
* point
* @param fastqFile
*/
private void DecisionTree(IFqFile fastqFile)
{
stopwatch.Start();
Boolean upper = false, lower = false;
int i = 0, j = 0;
for (i = 0; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = 0; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue > 'J')
{
upper = true;
goto search;
}
else if (qualityValue < ';')
{
lower = true;
goto search;
}
}
}
search:
if (upper == true)
{
upperTree(i, j);
}
else if (lower == true)
{
lowerTree(i, j);
}
}
/**
* This method outlines the first decision to test quality data and return whether it resides
* in the higher ASCII regions greater than character J or in the lower regions below this
* point
* @param fastqFile
*/
private void DecisionTree(IFqFile fastqFile)
{
stopwatch.Start();
Boolean upper = false, lower = false;
int i = 0, j = 0;
for (i = 0; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = 0; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue > 'J')
{
upper = true;
goto search;
}
else if (qualityValue < ';')
{
lower = true;
goto search;
}
}
}
search:
if (upper == true)
{
upperTree(i, j);
}
else if (lower == true)
{
lowerTree(i, j);
}
}
///<summary>
///Default constructor for the SaveFile class, accepts string to save and parameters for the savefiledialogue window
///</summary>
///<param name="output">The string to be saved</param>
///<param name="message">Message to be displayed on the save file dialogue window</param>
///<param name="filter">String to filter access to file types in the savefiledialogue window</param>
public SaveFile(IFqFile file, String message, FastqGUI o, String saveType, String filter = "Text File|*.txt|FastqFile|*.fq")
{
this.fqFile = file;
this.message = message;
this.filter = filter;
this.observer = o;
this.saveAction = saveType;
}
/// <summary>
/// Creates a fqFile_component_details class from the core information that is best still stored within the programs memory.
/// These classes populate a dictionary within the fqfilemap class where the component filename is their key.
/// </summary>
/// <param name="component">The component who's details are to be stored</param>
public void BuildFqFileMap(IFqFile component)
{
FqFile_Component_Details componentDetails = new FqFile_Component_Details();
componentDetails.ContructComponentDetails(component);
fqFileMap.GetFqFileComponentDetailsMap()[component.getFileName()] = componentDetails;
}
///<summary>
///Default constructor for the SaveFile class, accepts string to save and parameters for the savefiledialogue window
///</summary>
///<param name="output">The string to be saved</param>
///<param name="message">Message to be displayed on the save file dialogue window</param>
///<param name="filter">String to filter access to file types in the savefiledialogue window</param>
public SaveFile(IFqFile file, String message, FastqGUI o, String saveType, String filter = "Text File|*.txt|FastqFile|*.fq")
{
this.fqFile = file;
this.message = message;
this.filter = filter;
this.observer = o;
this.saveAction = saveType;
}
public SequencerDecisionTree(IFqFile aFastqFile)
{
ASSUMPTION_POINT = Preferences.getInstance().getAssumptionPref();
fastqFile = aFastqFile;
index = fastqFile.getFastqArraySize();
map = fastqFile.getMap();
Console.WriteLine("Starting to search for sequencer");
DecisionTree(fastqFile);
}
public SequencerDecisionTree(IFqFile aFastqFile)
{
ASSUMPTION_POINT = Preferences.getInstance().getAssumptionPref();
fastqFile = aFastqFile;
index = fastqFile.getFastqArraySize();
map = fastqFile.getMap();
Console.WriteLine("Starting to search for sequencer");
DecisionTree(fastqFile);
}
public IFqFile Parse()
{
if (IsStandardFormat == true)
{
FILE_FORMAT_TYPE = "Standard Fastq File Format";
fastqFile = ParseStandardFormat();
}
else if (IsMultiLineFormat == true)
{
FILE_FORMAT_TYPE = "Multi-Line Fastq File Format";
fastqFile = ParseMultiLineFormat();
}
return(fastqFile);
}
/// <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 override GenericFastqInputs perform(GenericFastqInputs inputs)
{
StreamWriter writer;
String extension = Path.GetExtension(inputs.SaveFileName);
String fileName = Path.GetFileNameWithoutExtension(inputs.SaveFileName);
String[] part = Path.GetFileNameWithoutExtension(inputs.FastqFile.getFileName()).Split('_');
String directory = Path.GetDirectoryName(inputs.SaveFileName);
String number = part[part.Length - 1];
String FullName = String.Format(@"{0}{1}{2}_{3}{4}", directory, Path.DirectorySeparatorChar, fileName, number, extension);
string COMMA_DELIMITER = ",";
string[] output;
IFqFile fqFile = inputs.FastqFile;
writer = new StreamWriter(FullName);
output = new string[] { "Sequence Index", "Header", "Total Nucleotides", "G Count", "C Count", "Misread Count", "Lower Threshold", "First Quartile",
"Median", "Mean", "Third Quartile", "Upper Threshold" };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
output = new string[] { fqSeq.getSeqIndex().ToString(), fqSeq.getSequenceHeader(), fqSeq.getFastqSeqSize().ToString(), fqSeq.getGCount().ToString(),
fqSeq.getCCount().ToString(), fqSeq.getNCount().ToString(), fqSeq.getLowerThreshold().ToString(),
fqSeq.getFirstQuartile().ToString(), fqSeq.getMedian().ToString(), fqSeq.getMean().ToString(),
fqSeq.getThirdQuartile().ToString(), fqSeq.getUpperThreshold().ToString(),
fqSeq.createSequenceString(fqFile.getMap()) };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
}
Console.WriteLine("Saving CSV TO: {0}", FullName);
writer.Flush();
writer.Close();
return(inputs);
}
private void SaveFastqAction(IFqFile fq, String fileName)
{
StreamWriter writer;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(40, "[CREATING FASTQ FORMAT]");
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
writer.Write(fqFile.getFastqSequenceByPosition(i).createFastqBlock(fqFile.getMap()));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
/// <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();
}
private void SaveCSVAction(IFqFile fq, String fileName)
{
StreamWriter writer;
string COMMA_DELIMITER = ",";
string[] output;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(30, "[CREATING CSV FORMAT]");
output = new string[] { "Sequence Index", "Header", "Total Nucleotides", "G Count", "C Count", "Misread Count", "Lower Threshold", "First Quartile",
"Median", "Mean", "Third Quartile", "Upper Threshold" };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
output = new string[] { fqSeq.getSeqIndex().ToString(), fqSeq.getSequenceHeader(), fqSeq.getFastqSeqSize().ToString(), fqSeq.getGCount().ToString(),
fqSeq.getCCount().ToString(), fqSeq.getNCount().ToString(), fqSeq.getLowerThreshold().ToString(),
fqSeq.getFirstQuartile().ToString(), fqSeq.getMedian().ToString(), fqSeq.getMean().ToString(),
fqSeq.getThirdQuartile().ToString(), fqSeq.getUpperThreshold().ToString(),
fqSeq.createSequenceString(fqFile.getMap()) };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
private void SaveFastaAction(IFqFile fq, String fileName)
{
saveWorker.ReportProgress(40, "[CREATING FASTA FORMAT]");
String output = fqFile.createFastaFormat("");
saveWorker.ReportProgress(100, "[FASTA FORMAT CREATED]");
StreamWriter writer;
try
{
writer = new StreamWriter(@fileName);
writer.Write(output);
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
private void SaveFastaAction(IFqFile fq, String fileName)
{
saveWorker.ReportProgress(40, "[CREATING FASTA FORMAT]");
String output = fqFile.createFastaFormat("");
saveWorker.ReportProgress(100, "[FASTA FORMAT CREATED]");
StreamWriter writer;
try
{
writer = new StreamWriter(@fileName);
writer.Write(output);
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
public IFqFile Parse()
{
if (IsStandardFormat == true)
{
FILE_FORMAT_TYPE = "Standard Fastq File Format";
fastqFile = ParseStandardFormat();
}
else if (IsMultiLineFormat == true)
{
FILE_FORMAT_TYPE = "Multi-Line Fastq File Format";
fastqFile = ParseMultiLineFormat();
}
return fastqFile;
}
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());
}
public SequencerDetermination(IFqFile fastqFile)
{
map = fastqFile.getMap();
sequencer(fastqFile);
}
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 SaveCSVAction(IFqFile fq, String fileName)
{
StreamWriter writer;
string COMMA_DELIMITER = ",";
string[] output;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(30, "[CREATING CSV FORMAT]");
output = new string[] {"Sequence Index", "Header", "Total Nucleotides", "G Count", "C Count", "Misread Count", "Lower Threshold", "First Quartile",
"Median", "Mean", "Third Quartile", "Upper Threshold" };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
output = new string[] { fqSeq.getSeqIndex().ToString(), fqSeq.getSequenceHeader(), fqSeq.getFastqSeqSize().ToString(), fqSeq.getGCount().ToString(),
fqSeq.getCCount().ToString(), fqSeq.getNCount().ToString(), fqSeq.getLowerThreshold().ToString(),
fqSeq.getFirstQuartile().ToString(), fqSeq.getMedian().ToString(), fqSeq.getMean().ToString(),
fqSeq.getThirdQuartile().ToString(), fqSeq.getUpperThreshold().ToString(),
fqSeq.createSequenceString(fqFile.getMap()) };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
public SequencerDetermination(IFqFile fastqFile)
{
map = fastqFile.getMap();
sequencer(fastqFile);
}
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();
}
/// <summary>
/// Creates a fqFile_component_details class from the core information that is best still stored within the programs memory.
/// These classes populate a dictionary within the fqfilemap class where the component filename is their key.
/// </summary>
/// <param name="component">The component who's details are to be stored</param>
public void BuildFqFileMap(IFqFile component)
{
FqFile_Component_Details componentDetails = new FqFile_Component_Details();
componentDetails.ContructComponentDetails(component);
fqFileMap.GetFqFileComponentDetailsMap()[component.getFileName()] = componentDetails;
}
private void SaveFastqAction(IFqFile fq, String fileName)
{
StreamWriter writer;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(40, "[CREATING FASTQ FORMAT]");
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
writer.Write(fqFile.getFastqSequenceByPosition(i).createFastqBlock(fqFile.getMap()));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
