/**
* 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);
}
}
private void solexaIllumina3(int startPosition, int startPos)
{
Boolean solexa = false;
int i, j;
Console.WriteLine("uppersearch - solexa illumina3");
for (i = startPosition; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = startPos; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue < '@')
{
solexa = true;
goto search;
}
else if (i == ASSUMPTION_POINT + startPosition)
{
sequencerType = "Illumina 1.3";
end(i);
goto search;
}
}
}
search:
if (solexa == true)
{
sequencerType = "Solexa";
end(i);
}
}
private void illuminaEightNine(int startPosition, int startPos)
{
Boolean illuminaEight = false;
int i = startPosition, j = startPos;
for (i = startPosition; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = startPos; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue < '#')
{
illuminaEight = true;
goto search;
}
else if (i == ASSUMPTION_POINT + startPosition)
{
sequencerType = "Illumina 1.9";
end(i);
goto search;
}
}
}
search:
if (illuminaEight == true)
{
sequencerType = "Illumina 1.8";
end(i);
}
}
public static Boolean ProtobufSerialize(FqSequence o, String fileName)
{
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
using (var file = File.Create(fileName))
{
Serializer.Serialize <FqSequence>(file, o);
sw.Stop();
Console.WriteLine("Protobuf Serilization Time: {0} of Filename: {1} ", sw.Elapsed, fileName);
return(true);
}
}
catch (IOException exception)
{
Console.WriteLine("Protobuf Serialization Failed: {0}", exception.StackTrace);
}
catch (System.Runtime.Serialization.SerializationException exception)
{
Console.WriteLine("Protobuf Serialization Failed: {0}", exception.StackTrace);
}
return(false);
}
public IFqFile ParseStandardFormat()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0)
{
continue;
}
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.Close();
}
return(fastqFile);
}
/// <summary>
/// Adds a FqSequence to the array and increments the index, contains provisions for increasing the size of the array
/// for overflow
/// </summary>
/// <param name="fqSeq"></param>
public override void addFastqSequence(FqSequence fqSeq)
{
fastqSeq[index] = fqSeq;
index++;
if (index >= LENGTH_SEQUENCE_ARRAY - 1)
{
LENGTH_SEQUENCE_ARRAY = LENGTH_SEQUENCE_ARRAY + LENGTH_SEQUENCE_ARRAY;
Array.Resize <FqSequence>(ref fastqSeq, (LENGTH_SEQUENCE_ARRAY));
}
}
public IFqFile parseByteFastq()
{
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
FqNucleotideRead fqRead = new FqNucleotideRead();
FqSequence fqSeq;
sw = new Stopwatch();
sw.Start();
const int LINES_IN_BLOCK = 4, HEADER_LINE = 0, SEQLINE = 1, INFO_LINE = 2, QUAL_LINE = 3, MAX_LINE = 250;
int lineIter = 0, bitIter = 1, seqIndex = 0;
byte[][] fqBlocks = new byte[4][]
{
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE]
};
for (int i = 0; i < byteArray.Length; i++)
{
if (byteArray[i] == CARRIDGE_RETURN)
{
fqBlocks[lineIter][0] = (byte)bitIter;
bitIter = 1;
lineIter++;
if (lineIter == LINES_IN_BLOCK)
{
lineIter = 0;
fqSeq = new FqSequence(seqIndex, System.Text.Encoding.ASCII.GetString(fqBlocks[HEADER_LINE]), System.Text.Encoding.ASCII.GetString(fqBlocks[INFO_LINE]), fqBlocks[SEQLINE][0]);
for (int j = 1; j < (fqBlocks[SEQLINE][0]); j++)
{
fqRead.resetFqNucleotideRead((char)fqBlocks[SEQLINE][j], (char)fqBlocks[QUAL_LINE][j]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
seqIndex++;
}
}
else
{
fqBlocks[lineIter][bitIter] = byteArray[i];
bitIter++;
}
}
Console.WriteLine("PARSED: File read in {0} s from byte array", sw.Elapsed);
return(fastqFile);
}
/// <summary>
/// Find sequences with a specific queried sequence.
/// </summary>
public override List <FqSequence> findSequence(String sequence)
{
List <FqSequence> foundSequences = new List <FqSequence>();
object locker = new object();
Parallel.For(0, index, i =>
{
FqSequence result = fastqSeq[i].findSequence(sequence, Fq_FILE_MAP);
if (result != null)
{
lock (locker)
foundSequences.Add(result);
}
});
Console.WriteLine("Found {0} Sequences Containing: {1}", foundSequences.Count, sequence);
return(foundSequences);
}
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);
}
/// <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);
}
}
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 static Boolean ProtobufSerialize(FqSequence o, String fileName)
{
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
using (var file = File.Create(fileName))
{
Serializer.Serialize<FqSequence>(file, o);
sw.Stop();
Console.WriteLine("Protobuf Serilization Time: {0} of Filename: {1} ", sw.Elapsed, fileName);
return true;
}
}
catch (IOException exception)
{
Console.WriteLine("Protobuf Serialization Failed: {0}", exception.StackTrace);
}
catch (System.Runtime.Serialization.SerializationException exception)
{
Console.WriteLine("Protobuf Serialization Failed: {0}", exception.StackTrace);
}
return false;
}
/*--------------Upper ASCII ISequencer Types-------------------*/
/**
* This method is created if the data set shows that the sequencer is likely from the
* solexa, illumina 1.3 or 1.5 branches. startPosition is the starting point to iterate
* through array
* @param startPosition
*/
private void upperTree(int startPosition, int startPos)
{
Boolean solexa = false, jointSolexaIllumina = false;
int i = startPosition, j = startPos;
Console.WriteLine("uppersearch - upper tree");
for (i = startPosition; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = startPos; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue < 'B')
{
jointSolexaIllumina = true;
goto search;
}
else if (qualityValue < '@')
{
solexa = true;
goto search;
}
else if (i == ASSUMPTION_POINT + startPosition)
{
sequencerType = "Illumina 1.5";
end(i);
goto search;
}
}
}
search:
if (solexa == true)
{
sequencerType = "Solexa";
end(i);
}
else if (jointSolexaIllumina == true)
{
this.solexaIllumina3(i, j);
}
}
private void sangerIlluminaEight(int startPosition, int startPos)
{
Boolean illumina8 = false;
int i, j;
for (i = startPosition; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = startPos; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue > 'I')
{
illumina8 = true;
goto search;
}
else if (i == ASSUMPTION_POINT + startPosition)
{
sequencerType = "Sanger";
end(i);
goto search;
}
}
}
search:
if (illumina8 == true)
{
sequencerType = "Illumina 1.8";
end(i);
}
}
/*-----------------Lower ASCII ISequencer Regions-------------------*/
private void lowerTree(int startPosition, int startPos)
{
Boolean sangerEight = false, illuminaEightNine = false;
int i = startPosition;
int j = startPos;
for (i = startPosition; i < index; i++)
{
fastqSeq = fastqFile.getFastqSequenceByPosition(i);
for (j = startPos; j < fastqSeq.getFastqSeqSize(); j++)
{
char qualityValue = map[fastqSeq.getFastqSeqAtPosition(j)].getQualityRead();
if (qualityValue < '#')
{
sangerEight = true;
goto search;
}
else if (qualityValue > 'I')
{
illuminaEightNine = true;
goto search;
}
else if (i == ASSUMPTION_POINT + startPosition)
{
sequencerType = "Illumina 1.9";
end(i);
goto search;
}
}
}
search:
if (sangerEight == true)
{
this.sangerIlluminaEight(i, j);
}
else if (illuminaEightNine == true)
{
this.illuminaEightNine(i, j);
}
}
public IEnumerable<FqFile_Component> ParseStandardFormatComponent()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
int blockNumber = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
FqFile_Component fastqFileComponent = new FqFile_Component();
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0) continue;
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFileComponent.addFastqSequence(fqSeq);
nLine += 3;
blockNumber ++;
if (blockNumber == FqFileMap.FQ_BLOCK_LIMIT)
{
yield return fastqFileComponent;
blockNumber = 0;
fastqFileComponent = new FqFile_Component();
}
}
yield return fastqFileComponent;
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.FlushAsync();
fileReader.Close();
}
}
public IFqFile ParseStandardFormat()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 4 != 0) continue;
String seqlist = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, seqlist.Length);
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
}
finally
{
fileReader.Close();
}
return fastqFile;
}
public IFqFile parseByteFastq()
{
//fastqFile = FqFileSpecifier.getInstance().getFqFile(Preferences.getInstance().getMultiCoreProcessing());
fastqFile.setFastqFileName(fileName);
FqNucleotideRead fqRead = new FqNucleotideRead();
FqSequence fqSeq;
sw = new Stopwatch();
sw.Start();
const int LINES_IN_BLOCK = 4, HEADER_LINE = 0, SEQLINE = 1, INFO_LINE = 2, QUAL_LINE = 3, MAX_LINE = 250;
int lineIter = 0, bitIter = 1, seqIndex = 0;
byte[][] fqBlocks = new byte[4][]
{
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE],
new byte[MAX_LINE]
};
for (int i = 0; i < byteArray.Length; i++)
{
if (byteArray[i] == CARRIDGE_RETURN)
{
fqBlocks[lineIter][0] = (byte) bitIter;
bitIter = 1;
lineIter++;
if (lineIter == LINES_IN_BLOCK)
{
lineIter = 0;
fqSeq = new FqSequence(seqIndex, System.Text.Encoding.ASCII.GetString(fqBlocks[HEADER_LINE]), System.Text.Encoding.ASCII.GetString(fqBlocks[INFO_LINE]), fqBlocks[SEQLINE][0]);
for (int j = 1; j < (fqBlocks[SEQLINE][0]); j++)
{
fqRead.resetFqNucleotideRead((char)fqBlocks[SEQLINE][j], (char)fqBlocks[QUAL_LINE][j]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
fastqFile.addFastqSequence(fqSeq);
seqIndex++;
}
}
else
{
fqBlocks[lineIter][bitIter] = byteArray[i];
bitIter++;
}
}
Console.WriteLine("PARSED: File read in {0} s from byte array", sw.Elapsed);
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 IEnumerable <FqFile_Component> ParseMultiLineFormatComponent()
{
sw = new Stopwatch();
sw.Start();
int seqIndex = 0;
int blockNumber = 0;
BufferedStream bs;
StreamReader reader;
try
{
bs = new BufferedStream(fileReader);
reader = new StreamReader(bs, System.Text.Encoding.ASCII);
if (IsFastqFile == true)
{
FastqController.getInstance().GetFqFileMap().FastqFileFormatType = FILE_FORMAT_TYPE;
FqNucleotideRead fqRead = new FqNucleotideRead(' ', ' ');
FqFile_Component fastqFileComponent = new FqFile_Component();
long nLine = -1L;
while ((fastqHeader = reader.ReadLine()) != null)
{
nLine++;
if (nLine % 6 != 0)
{
continue;
}
String seqlist = reader.ReadLine();
String seqlist2 = reader.ReadLine();
String infoHeader = reader.ReadLine();
String qscore = reader.ReadLine();
String qscore2 = reader.ReadLine();
fqSeq = new FqSequence(seqIndex, fastqHeader, infoHeader, (seqlist.Length + seqlist2.Length));
seqIndex++;
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist[i], qscore[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
if (seqlist2.Length > 0 && (seqlist2.Length == qscore2.Length))
{
for (int i = 0; i < (seqlist.Length); i++)
{
fqRead.resetFqNucleotideRead(seqlist2[i], qscore2[i]);
int hashcode = fqRead.getProxyCode();
fqSeq.addNucleotideRead(hashcode);
}
}
fastqFile.addFastqSequence(fqSeq);
nLine += 3;
blockNumber++;
if (blockNumber == FqFileMap.FQ_BLOCK_LIMIT)
{
yield return(fastqFileComponent);
blockNumber = 0;
fastqFileComponent = new FqFile_Component();
}
}
yield return(fastqFileComponent);
}
}
finally
{
fileReader.Close();
}
sw.Stop();
Console.WriteLine("Time to Parse File: " + sw.Elapsed + "s");
}
abstract public void addFastqSequence(FqSequence fqSeq);
public abstract void addFastqSequence(FqSequence fqSeq);
/// <summary>
/// Adds a FqSequence to the array and increments the index, contains provisions for increasing the size of the array
/// for overflow
/// </summary>
/// <param name="fqSeq"></param>
public override void addFastqSequence(FqSequence fqSeq)
{
fastqSeq[index] = fqSeq;
index++;
if(index >= LENGTH_SEQUENCE_ARRAY - 1)
{
LENGTH_SEQUENCE_ARRAY = LENGTH_SEQUENCE_ARRAY + LENGTH_SEQUENCE_ARRAY;
Array.Resize<FqSequence>(ref fastqSeq, (LENGTH_SEQUENCE_ARRAY));
}
}
