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 static string ProcessChromosome(Dictionary <string, int> chromRefIds, string outMultiPath, List <string> taskDirectories,
string chrom, GeminiMultiOptions options)
{
// TODO either officially deprecate non-multiprocess-processing and remove this, or consolidate this with the Gemini calling code from Gemini/Program.cs
var outdir = Path.Combine(outMultiPath, chrom);
var refId = chromRefIds[chrom];
var intermediate = string.IsNullOrEmpty(options.GeminiSampleOptions.IntermediateDir)
? null
: Path.Combine(options.GeminiSampleOptions.IntermediateDir, chrom);
var geminiSampleOptions = new GeminiSampleOptions
{
InputBam = options.InputBam,
OutputFolder = outdir,
OutputBam = Path.Combine(outdir, "out.bam"),
IntermediateDir = intermediate,
RefId = refId
};
// Gemini defaults different than stitcher defaults
options.StitcherOptions.NifyUnstitchablePairs = false;
// Set stitcher pair-filter-level duplicate filtering if skip and remove dups, to save time
options.StitcherOptions.FilterDuplicates = options.GeminiOptions.SkipAndRemoveDups;
var dataSourceFactory = new GeminiDataSourceFactory(options.StitcherOptions, options.GeminiOptions.GenomePath,
options.GeminiOptions.SkipAndRemoveDups, refId,
Path.Combine(outdir, "Regions.txt"), debug: options.GeminiOptions.Debug);
var dataOutputFactory = new GeminiDataOutputFactory(options.StitcherOptions.NumThreads);
var samtoolsWrapper = new SamtoolsWrapper(options.GeminiOptions.SamtoolsPath, options.GeminiOptions.IsWeirdSamtools);
var geminiWorkflow = new GeminiWorkflow(dataSourceFactory, dataOutputFactory,
options.GeminiOptions, geminiSampleOptions, options.RealignmentOptions, options.StitcherOptions, options.OutputDirectory, options.RealignmentAssessmentOptions, options.IndelFilteringOptions, samtoolsWrapper);
Directory.CreateDirectory(outdir);
geminiWorkflow.Execute();
//var logger = new Illumina.CG.Common.Logging.Logger(taskLogDir, $"GeminiTaskLog_{chrom}.txt");
//var task = _taskCreator.GetCliTask(cmdLineList.ToArray(), chrom, exePath, outdir, chromRefIds[chrom], logger,
// string.IsNullOrEmpty(_options.GeminiSampleOptions.IntermediateDir)
// ? null
// : Path.Combine(_options.GeminiSampleOptions.IntermediateDir, chrom));
//tasks.Add(task);
Console.WriteLine($"Completed Gemini Workflow for {chrom}");
var path = (Path.Combine(outdir, "merged.bam.sorted.bam"));
taskDirectories.Add(outdir);
//paths[refId] = path;
return(path);
}
