/**
* 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 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);
}
}
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);
}
}
/*--------------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);
}
}
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());
}