/// <summary>
/// Perform both distribution and nucleotide tests on fqfile component
/// </summary>
public override void performJointTests()
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
totalNucleotides();
resetCounts();
fillDistributionList();
int subZeroOffset = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getSubZeroQualities();
Parallel.For(0, index, new ParallelOptions {
MaxDegreeOfParallelism = (Preferences.getInstance().getCoresToUse())
},
// Initialize the local states
() => new FqSequence_IO(sequencerType, "Sequence Tests", this),
// Accumulate the thread-local computations in the loop body
(i, loop, syncLists) =>
{
for (int j = 0; j < fastqSeq[i].getFastqSeqSize(); j++)
{
char nucleotide = Fq_FILE_MAP[fastqSeq[i].getFastqSeqAtPosition(j)].getNucleotide();
if (nucleotide == 'N')
{
Interlocked.Increment(ref nCount);
}
else if (nucleotide == 'C')
{
Interlocked.Increment(ref cCount);
}
else if (nucleotide == 'G')
{
Interlocked.Increment(ref gCount);
}
int qualityScore = Fq_FILE_MAP[fastqSeq[i].getFastqSeqAtPosition(j)].getQualityScore();
int currentPop = syncLists.distributes[(qualityScore + subZeroOffset)];
syncLists.distributes[(qualityScore + subZeroOffset)] = (currentPop + 1);
}
return(syncLists);
},
syncLists => {
Object locker = new object();
lock (locker)
{
this.CombineDistributionLists(syncLists.distributes);
}
}
);
nPercent = (((double)nCount / totalNucs) * 100);
cPercent = (((double)cCount / totalNucs) * 100);
gPercent = (((double)gCount / totalNucs) * 100);
stopwatch.Stop();
Console.Write("Joint tests completed: " + stopwatch.Elapsed + "\n");
}
/// <summary>
/// Performs a distribution test on the quality reads of the fastq file component
/// </summary>
/// <returns>A list that outlines the distribution of qualities within this file component</returns>
public override List <int> performDistributionTest()
{
fillDistributionList();
int subZeroOffset = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getSubZeroQualities();
Parallel.For(0, index, new ParallelOptions {
MaxDegreeOfParallelism = (Preferences.getInstance().getCoresToUse())
},
// Initialize the local states
() => new FqSequence_IO(sequencerType, "Sequence Tests", this),
// Accumulate the thread-local computations in the loop body
(i, loop, syncLists) =>
{
for (int j = 0; i < fastqSeq[i].getFastqSeqSize(); j++)
{
int qualityScore = Fq_FILE_MAP[fastqSeq[i].getFastqSeqAtPosition(j)].getQualityScore();
int currentPop = syncLists.distributes[(qualityScore + subZeroOffset)];
syncLists.distributes[(qualityScore + subZeroOffset)] = (currentPop + 1);
}
return(syncLists);
},
syncLists =>
{
Object locker = new object();
lock (locker)
{ this.CombineDistributionLists(syncLists.distributes); }
});
return(distribution);
}
/// <summary>
/// Initializes the distribution list for the object.
/// </summary>
private void fillDistributionList()
{
distribution = new List <int>(SequencerDiscriminator.getSequencerSpecifier(sequencerType).getDistributionSpread());
for (int j = 0; j <= SequencerDiscriminator.getSequencerSpecifier(sequencerType).getDistributionSpread(); j++)
{
distribution.Add(0);
}
}
public void deconstructHeader(String sequencerType)
{
MachineName = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getMachineName(Header);
FlowCellLane = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getFlowCellLane(Header);
TileNumber = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getTileNumber(Header);
XCoord = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getXCoOrd(Header);
YCoord = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getYCoOrd(Header);;
}
/// <summary>
/// Draws a distribution for the quality scores for the FastqComponent_Details handle within this class
/// </summary>
public void DrawDistribution()
{
Console.WriteLine("Drawing new sequence length distribution!");
double[] sequenceDistribution = componentDetails.Distribution.Select(i => (double)i).ToArray();
double[] x = new double[sequenceDistribution.Length];
int count = 0;
for (int i = 0; i < x.Length; i++)
{
x[i] = count - SequencerDiscriminator.getSequencerSpecifier(componentDetails.sequencerType).getSubZeroQualities();
count++;
}
Size size = graphControl.ClientSize;
Rectangle rect = new Rectangle();
rect.Size = size;
// This is to remove all plots
graphControl.GraphPane = new GraphPane();
graphControl.GraphPane.CurveList.Clear();
graphControl.GraphPane.Rect = rect;
// GraphPane object holds one or more Curve objects (or plots)
GraphPane myPane = graphControl.GraphPane;
myPane.Title.Text = "Quality Distribution " + componentDetails.getGraphName();
// set X and Y axis titles
myPane.XAxis.Title.Text = "Quality";
myPane.YAxis.Title.Text = "Nucleotide Count";
// PointPairList holds the data for plotting, X and Y arrays
PointPairList spl1 = new PointPairList(x, sequenceDistribution);
// Add bars to myPane object
BarItem myBar1 = myPane.AddBar(FastqChartTypes.SequenceLengthDistribution.ToString(), spl1, Color.Red);
LineItem myLine1 = myPane.AddCurve(FastqChartTypes.SequenceLengthDistribution.ToString(), spl1, Color.Red, SymbolType.None);
myLine1.Line.Width = 1.0F;
// I add all three functions just to be sure it refeshes the plot.
graphControl.AxisChange();
graphControl.Invalidate();
graphControl.Refresh();
}
public FqSequence_IO(String sequencerType, String taskType, FqFile_Component fqFile)
{
if (taskType == SEQUENCE_TESTS_TASK)
{
distributes = new List <int>(40);
for (int j = 0; j <= SequencerDiscriminator.getSequencerSpecifier(sequencerType).getDistributionSpread(); j++)
{
distributes.Add(0);
}
perSeqQuals = new int[fqFile.getMaxSeqSize()];
subZeroOffset = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getSubZeroQualities();
}
else if (taskType == ADAPTER_TASK)
{
adapters = Adapters.getInstance().getAdaptersList();
removedAdapters = null;
}
}
public static void register()
{
//SequencerSpecifier value = sequencer as SequencerSpecifier;
SequencerDiscriminator.register(sequencerName, sequencer);
}
public static void register()
{
SequencerDiscriminator.register(sequencerName, sequencer);
}
public void calculateQualityScore(string sequencerType)
{
qualityScore = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getQualityScore(qualityRead);
PHREDScore = SequencerDiscriminator.getSequencerSpecifier(sequencerType).getPHREDScore(qualityScore);
}
