public FqSequence_IO Tests(Dictionary <int, FqNucleotideRead> map, FqSequence_IO inputs)
{
int qualitySum = 0;
List <int> qualities = new List <int>();
resetCounts();
for (int i = 0; i < index; i++)
{
char nucleotide = map[fastqSequence[i]].getNucleotide();
if (nucleotide == 'N')
{
NCount++;
}
else if (nucleotide == 'C')
{
CCount++;
}
else if (nucleotide == 'G')
{
GCount++;
}
int qualityScore = map[fastqSequence[i]].getQualityScore();
qualitySum += qualityScore;
qualities.Add(qualityScore);
int currentPop = inputs.distributes[(qualityScore + inputs.subZeroOffset)];
inputs.distributes[(qualityScore + inputs.subZeroOffset)] = (currentPop + 1);
}
inputs.cCount = CCount;
inputs.gCount = GCount;
inputs.nCount = NCount;
for (int i = 0; i < qualities.Count; i++)
{
inputs.perSeqQuals[i] = qualities[i];
}
inputs.sequenceLength = index;
qualities.Sort();
int size = qualities.Count;
Mean = (double)qualitySum / SEQUENCE_LENGTH;
Median = (int)qualities[(size / 2)];
ThirdQuartile = (int)qualities[((size / 4) * 3)];
FirstQuartile = (int)qualities[((size / 4))];
LowerThreshold = (int)qualities[0];
UpperThreshold = (int)qualities[size - 1];
return(inputs);
}
public FqSequence_IO Tests(Dictionary<int, FqNucleotideRead> map, FqSequence_IO inputs)
{
int qualitySum = 0;
List<int> qualities = new List<int>();
resetCounts();
for (int i = 0; i < index; i++)
{
char nucleotide = map[fastqSequence[i]].getNucleotide();
if (nucleotide == 'N') NCount++;
else if (nucleotide == 'C') CCount++;
else if (nucleotide == 'G') GCount++;
int qualityScore = map[fastqSequence[i]].getQualityScore();
qualitySum += qualityScore;
qualities.Add(qualityScore);
int currentPop = inputs.distributes[(qualityScore + inputs.subZeroOffset)];
inputs.distributes[(qualityScore + inputs.subZeroOffset)] = (currentPop + 1);
}
inputs.cCount = CCount;
inputs.gCount = GCount;
inputs.nCount = NCount;
for (int i = 0; i < qualities.Count; i++)
inputs.perSeqQuals[i] = qualities[i];
inputs.sequenceLength = index;
qualities.Sort();
int size = qualities.Count;
Mean = (double)qualitySum / SEQUENCE_LENGTH;
Median = (int)qualities[(size / 2)];
ThirdQuartile = (int)qualities[((size / 4) * 3)];
FirstQuartile = (int)qualities[((size / 4))];
LowerThreshold = (int)qualities[0];
UpperThreshold = (int)qualities[size - 1];
return inputs;
}
