//wrapper should now handle all throwing and catching..
protected override void ProgramExecution()
{
var optionsUsed = _appOptionParser.ParsingResult.OptionsUsed;
var doNotPassToSubprocess = new List <string>()
{
"outFolder", "numProcesses", "exePath", "intermediateDir", "multiprocess", "chromosomes"
};
var cmdLineList = MultiProcessHelpers.GetCommandLineWithoutIgnoredArguments(optionsUsed, doNotPassToSubprocess);
var refNameMapping = new Dictionary <string, int>();
using (var bamReader = new BamReader(_options.InputBam))
{
var chroms = bamReader.GetReferenceNames();
foreach (var referenceName in chroms)
{
if (_options.Chromosomes != null && !_options.Chromosomes.ToList().Contains(referenceName))
{
continue;
}
refNameMapping.Add(referenceName, bamReader.GetReferenceIndex(referenceName));
}
}
var taskManager = new CliTaskManager(_options.NumProcesses);
var geminiProcessor = new GeminiMultiProcessor(_options, new CliTaskCreator());
var samtoolsWrapper = new SamtoolsWrapper(_options.GeminiOptions.SamtoolsPath, _options.GeminiOptions.IsWeirdSamtools);
geminiProcessor.Execute(taskManager, refNameMapping, cmdLineList, samtoolsWrapper);
}
private List <string> ExecuteChromosomeJobs(Dictionary <string, int> chromRefIds,
string outMultiPath, List <string> taskDirectories)
{
var orderedChroms = MultiProcessHelpers.GetOrderedChromosomes(chromRefIds).ToList();
ConcurrentQueue <string> input = new ConcurrentQueue <string>(orderedChroms);
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var tasks = new List <Task>();
var pathsArray = new string[chromRefIds.Max(x => x.Value) + 1];
using (var concurrencySemaphore = new SemaphoreSlim(_options.NumProcesses))
{
foreach (var chrom in orderedChroms)
{
{
var options = new GeminiMultiOptions()
{
StitcherOptions = (_options.StitcherOptions.DeepCopy()),
GeminiSampleOptions = (_options.GeminiSampleOptions.DeepCopy()),
IndelFilteringOptions =
(_options.IndelFilteringOptions.DeepCopy()),
RealignmentAssessmentOptions =
(_options.RealignmentAssessmentOptions.DeepCopy()),
RealignmentOptions = (_options.RealignmentOptions.DeepCopy()),
GeminiOptions = (_options.GeminiOptions.DeepCopy()),
InputBam = _options.InputBam,
OutputDirectory = _options.OutputDirectory
};
Console.WriteLine($"Waiting to launch job for chrom {chrom}");
Console.WriteLine($"Launching job for chrom {chrom}");
concurrencySemaphore.Wait();
tasks.Add(Task.Factory.StartNew(() =>
{
try
{
pathsArray[chromRefIds[chrom]] = ProcessChromosome(chromRefIds, outMultiPath, taskDirectories, chrom, options);
}
finally
{
concurrencySemaphore.Release();
}
}));
}
}
Logger.WriteToLog("Launched all tasks.");
Task.WaitAll(tasks.ToArray());
return(pathsArray.Where(x => x != null).ToList());
}
}
private List <string> ExecuteChromosomeJobs(ICliTaskManager cliTaskManager, Dictionary <string, int> chromRefIds, List <string> cmdLineList,
string outMultiPath, string taskLogDir, string exePath, List <string> taskDirectories)
{
var tasks = new List <ICliTask>();
var paths = new List <string>();
//var loggers = new List<Illumina.CG.Common.Logging.Logger>();
foreach (var chrom in MultiProcessHelpers.GetOrderedChromosomes(chromRefIds))
{
var outdir = Path.Combine(outMultiPath, chrom);
//var logger = new Illumina.CG.Common.Logging.Logger(taskLogDir, $"GeminiTaskLog_{chrom}.txt");
//loggers.Add(logger);
var task = _taskCreator.GetCliTask(cmdLineList.ToArray(), chrom, exePath, outdir, chromRefIds[chrom]);
tasks.Add(task);
paths.Add(Path.Combine(outdir, "merged.bam.sorted.bam"));
taskDirectories.Add(outdir);
}
cliTaskManager.Process(tasks);
foreach (var task in tasks)
{
Logger.WriteToLog($"Completed task {task.Name} with exit code {task.ExitCode}.");
}
if (tasks.Any(x => x.ExitCode != 0))
{
foreach (var failedTask in tasks.Where(x => x.ExitCode != 0))
{
Logger.WriteWarningToLog($"Processing failed for {failedTask.Name}. See error log for details.");
}
throw new Exception($"Application failed: {tasks.Count(x => x.ExitCode != 0)} tasks failed.");
}
Logger.WriteToLog($"Completed {tasks.Count} tasks.");
return(paths);
//try
//{
// foreach (var logger in loggers)
// {
// logger.Dispose();
// }
//}
//catch (Exception e)
//{
// Logger.WriteExceptionToLog(
// new Exception($"Error encountered during logging cleanup step (after individual analysis completion).", e));
//}
}