/*
* 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());
}
