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));
//}
}
public void Execute(ICliTaskManager cliTaskManager, Dictionary <string, int> chromRefIds, List <string> cmdLineList, ISamtoolsWrapper samtoolsWrapper)
{
var bamFile = _options.InputBam;
var outMultiPath = _options.OutputDirectory;
var exePath = _options.ExePath;
List <string> paths;
var taskDirectories = new List <string>();
var taskLogDir = Path.Combine(outMultiPath, "TaskLogs");
if (_options.MultiProcess)
{
paths = ExecuteChromosomeJobs(cliTaskManager, chromRefIds, cmdLineList, outMultiPath, taskLogDir, exePath, taskDirectories);
}
else
{
paths = ExecuteChromosomeJobs(chromRefIds, outMultiPath,
taskDirectories);
}
var outBamName = Path.GetFileNameWithoutExtension(bamFile) + ".PairRealigned.bam";
MergeAndFinalizeBam(paths, samtoolsWrapper, outMultiPath,
outBamName);
try
{
CleanUp(outMultiPath, taskDirectories, taskLogDir);
}
catch (Exception e)
{
Logger.WriteExceptionToLog(new Exception($"Error encountered during cleanup step (after analysis completion).", e));
}
}
