/// <summary>
/// Determines whether a read satisfies the conditions to be discarded.
/// i.e. Does it meet the minimum mean quality score requirements?
/// </summary>
/// <param name="seqObj">A sequence object</param>
/// <returns>True if it does not meet the minimum mean and thus
/// will be discarded. False, otherwise.</returns>
public override bool CanDiscard(ISequence seqObj)
{
var myMean = QualityScoreAnalyzer.GetMeanFromBytes(
((QualitativeSequence)seqObj).QualityScores.ToArray()
);
if (myMean < MeanQualityThreshold)
{
return(true);
}
return(false);
}
/// <summary>
/// Implement the Maximum Contiguous Subsequence Sum alogirthm.
/// Source: http://www.cs.ucf.edu/~reinhard/classes/cop3503/lectures/AlgAnalysis04.pdf
/// Maximum Subarray Problem: http://en.wikipedia.org/wiki/Maximum_subarray_problem
///
/// Find the subsequence with the maximum sum of differences between the actual
/// base quality score and the given cutoff score.
/// </summary>
/// <param name="seqObj">The sequence object to be trimmed</param>
/// <returns>A new sequence object with trimmed sequence. Or null if a maximum subsequence
/// cannot be found (i.e. quality scores are below the cutoff)</returns>
public override ISequence Trim(ISequence seqObj)
{
byte[] scores = ((QualitativeSequence)seqObj).QualityScores.ToArray();
scores = QualityScoreAnalyzer.ConvertToPhred(scores, ((QualitativeSequence)seqObj).FormatType);
// Implement maximum sum segment algorithm.
int start = 0;
int sum = 0;
int maxSum = 0;
int maxStart = 0;
int maxEnd = -1;
for (int i = 0; i < scores.Length; i++)
{
sum += scores[i] - QualityThreshold;
// If sum is negative, the new subsequence resets from the next position.
if (sum < 0 && TrimFromStart)
{
start = i + 1;
sum = 0; // reset the sum to start the new subsequence
}
if (sum > maxSum)
{
maxSum = sum;
maxStart = start;
maxEnd = i;
}
}
// Return null if a maximum subsequence cannot be found
if (maxStart > maxEnd)
{
return(null);
}
var newLength = maxEnd - maxStart + 1;
// Also return null if the new trim length is less than the required minimum length
if (newLength < MinLength)
{
return(null);
}
var newSeqObj = seqObj.GetSubSequence(maxStart, newLength);
newSeqObj.ID = seqObj.ID;
return(newSeqObj);
}
/// <summary>
/// Consructor for creating plots from QualityScoreAnalyzer data
/// </summary>
/// <param name="analyzer">QualityScoreAnalyzer object that has been processed</param>
public QualityScorePlotter(QualityScoreAnalyzer analyzer)
{
if (analyzer == null)
{
throw new ArgumentNullException("analyzer");
}
if (!analyzer.HasRunContentByPosition)
{
throw new ArgumentException("QualityScoreAnalyzer object has not processed input data yet.");
}
this.Analyzer = analyzer;
this.titleBanner = MakeTitleBanner(Path.GetFileName(this.Analyzer.FileName), this.Analyzer.Count);
}
/// <summary>
/// Constructor that is called by the GUI. Provides BackgroundWorker and DoWorkEventArgs parameters that
/// are used to halt an operation if a Cancel event is fired.
/// </summary>
/// <param name="analyzer">QualityScoreAnalyzer object that has been processed</param>
/// <param name="worker">Background working thread (used by GUI)</param>
/// <param name="e">Worker event arguments</param>
public QualityScorePlotter(QualityScoreAnalyzer analyzer, BackgroundWorker worker, DoWorkEventArgs e)
: this(analyzer)
{
this.worker = worker;
this.workerArgs = e;
}
