/// <summary>
/// Updates the status of the masurca assembler. If it has either errored out (-1) or is completed (last step), it will not change the status.
/// </summary>
/// <param name="client">The current SSH client session.</param>
/// <param name="genomeModel">The model of the particular job.</param>
private static void CheckMasurcaStep(SshClient client, GenomeModel genomeModel)
{
if (string.IsNullOrEmpty(ErrorHandling.error) &&
!genomeModel.MasurcaCurrentStep.Equals(-1) &&
!genomeModel.MasurcaCurrentStep.Equals(StepDescriptions.GetMasurcaStepList().Last().step))
{
if (LinuxCommands.DirectoryHasFiles(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed)))
{
int currentMasurcaStep = LinuxCommands.GetCurrentStep(client, Accessors.GetMasurcaOutputPath(genomeModel.Seed), StepDescriptions.GetMasurcaStepList());
// Provided we didn't encounter an error, set the status of masurca and the job.
if (currentMasurcaStep != -1)
{
genomeModel.MasurcaCurrentStep = currentMasurcaStep;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), currentMasurcaStep);
}
else
{
StepDescriptions.SetMasurcaError(client, genomeModel);
}
}
// Either masurca hasn't started or it has but no files have been created yet.
else
{
genomeModel.MasurcaCurrentStep = 1;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), 1);
}
}
}
/// <summary>
/// Sets default values if the user decided not to enter any information for optional values in the wizard.
/// </summary>
/// <param name="genomeModel">The model data for a particular job.</param>
/// <returns>Returns the new job model with the default values.</returns>
public static GenomeModel SetDefaultMasurcaValues(GenomeModel genomeModel)
{
// If they don't have jump reads.
if (genomeModel.JumpReads == false)
{
genomeModel.JumpLength = 0;
}
// If they don't have paired-end reads.
if (genomeModel.PEReads == false)
{
genomeModel.PairedEndLength = 0;
}
if (genomeModel.MasurcaMean == null)
{
genomeModel.MasurcaMean = 180;
}
if (genomeModel.MasurcaStdev == null)
{
genomeModel.MasurcaStdev = 20;
}
// We don't specify anything here. If it is null, we set it to AUTO in the masurca method of the config builder.
if (genomeModel.MasurcaGraphKMerValue == null)
{
if (genomeModel.MasurcaKMerErrorCount == null)
{
genomeModel.MasurcaKMerErrorCount = 1;
}
}
if (genomeModel.MasurcaThreadNum == null)
{
genomeModel.MasurcaThreadNum = 20;
}
genomeModel.MasurcaCurrentStep = 1;
genomeModel.MasurcaStatus = StepDescriptions.GetCurrentStepDescription(StepDescriptions.GetMasurcaStepList(), 1);
return(genomeModel);
}