/// <summary>
/// This executes the discarding of reads on a background thread
/// </summary>
/// <param name="sender">BackgoundWorker instance</param>
/// <param name="e">DoWorkEvent arguments</param>
private void DoDiscardReads(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
if (worker != null)
{
try
{
Discarder myDiscarder = null;
FilterToolArgs args = null;
if (e.Argument is DiscardByLengthArgs)
{
args = e.Argument as DiscardByLengthArgs;
myDiscarder = ((DiscardByLengthArgs)args).discarder;
// If possible, verify that the discard length is not larger than the maximum read length.
MessageBoxResult tooLargeReadLength = TryConfirmLargeReadLength(args.InputInfo.Filename, (myDiscarder as DiscardByLength).MinLengthThreshold);
if (tooLargeReadLength == MessageBoxResult.Cancel)
{
e.Cancel = true;
return;
}
}
else if (e.Argument is DiscardByMeanQualityArgs)
{
args = e.Argument as DiscardByMeanQualityArgs;
myDiscarder = (e.Argument as DiscardByMeanQualityArgs).discarder;
}
else
{
args = e.Argument as DiscardByRegexArgs;
myDiscarder = (e.Argument as DiscardByRegexArgs).discarder;
}
myDiscarder.DiscardReads();
// Report results
string report = string.Format(Resource.DiscardReport, myDiscarder.DiscardCount, myDiscarder.Counted);
this.OpenInExplorer(args.OutputFilename);
e.Result = report.ToString();
}
catch (Exception ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
}
}
/// <summary>
/// This event is raised when the user selects to run the discard tool
/// after specifying all the required input parameters.
/// </summary>
/// <param name="sender">DiscardToolDialog window</param>
/// <param name="e">Discard arguments</param>
private void OnDiscardRunClick(object sender, FilterToolArgs e)
{
run = new RunProgressDialog(true);
run.ProgressText = "Discarding reads...";
run.StartRun += new EventHandler(this.OnRunDiscardStarted);
run.CancelRun += new EventHandler(this.OnCancelAnalysisClicked);
run.Args = e;
run.Owner = this;
this.IsEnabled = false;
run.ShowDialog();
this.IsEnabled = true;
}
/// <summary>
/// This executes the trimming of reads as a background thread.
/// </summary>
/// <param name="sender">BackgoundWorker instance</param>
/// <param name="e">DoWorkEvent arguments</param>
private void DoTrimReads(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
if (worker != null)
{
try
{
Trimmer myTrimmer = null;
FilterToolArgs args = null;
if (e.Argument is TrimByLengthArgs)
{
args = e.Argument as TrimByLengthArgs;
myTrimmer = (e.Argument as TrimByLengthArgs).trimmer;
// If possible, verify that the trim length is not larger than the maximum read length, if it
// is known (e.g. if a QC analysis was run just before Trim was called).
if ((myTrimmer as TrimByLength).TrimLength >= 1)
{
MessageBoxResult tooLargeReadLength = TryConfirmLargeReadLength(args.InputInfo.Filename,
Convert.ToInt64(Math.Round((myTrimmer as TrimByLength).TrimLength)));
if (tooLargeReadLength == MessageBoxResult.Cancel)
{
e.Cancel = true;
return;
}
}
}
else if (e.Argument is TrimByQualityArgs)
{
args = e.Argument as TrimByQualityArgs;
myTrimmer = (e.Argument as TrimByQualityArgs).trimmer;
}
else
{
args = e.Argument as TrimByRegexArgs;
myTrimmer = (e.Argument as TrimByRegexArgs).trimmer;
}
myTrimmer.Worker = worker;
myTrimmer.WorkerArgs = e;
myTrimmer.TrimAll();
// Report results
StringBuilder report = new StringBuilder();
report.AppendLine(string.Format(Resource.TrimReport, myTrimmer.TrimCount, myTrimmer.Counted));
report.AppendLine(string.Format(Resource.DiscardReport, myTrimmer.DiscardCount, myTrimmer.Counted));
this.OpenInExplorer(args.OutputFilename);
e.Result = report.ToString();
}
catch (ArgumentNullException ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
catch (Exception ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
}
}
