public GeminiApplicationOptions()
{
StitcherOptions = new StitcherOptions();
GeminiSampleOptions = new GeminiSampleOptions();
IndelFilteringOptions = new IndelFilteringOptions();
RealignmentAssessmentOptions = new RealignmentAssessmentOptions();
RealignmentOptions = new RealignmentOptions();
GeminiOptions = new GeminiOptions();
}
public DataflowReadEvaluator(GeminiOptions geminiOptions,
IGeminiDataSourceFactory dataSourceFactory, GeminiSampleOptions geminiSampleOptions, IGeminiDataOutputFactory dataOutputFactory, IBlockFactorySource blockFactorySource)
{
_geminiOptions = geminiOptions;
_dataSourceFactory = dataSourceFactory;
_geminiSampleOptions = geminiSampleOptions;
_dataOutputFactory = dataOutputFactory;
_blockFactorySource = blockFactorySource;
}
public static GeminiSampleOptions DeepCopy(this GeminiSampleOptions options)
{
return(new GeminiSampleOptions()
{
InputBam = options.InputBam,
IntermediateDir = options.IntermediateDir,
OutputBam = options.OutputBam,
OutputFolder = options.OutputFolder,
RefId = options.RefId
});
}
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);
}
public BlockFactorySource(StitcherOptions stitcherOptions, GeminiOptions geminiOptions, Dictionary <int, string> refIdMapping, BamRealignmentFactory bamRealignmentFactory,
IGeminiDataSourceFactory dataSourceFactory, GeminiSampleOptions geminiSampleOptions, RealignmentOptions realignmentOptions, IGeminiFactory geminiFactory)
{
_stitcherOptions = stitcherOptions;
_geminiOptions = geminiOptions;
_refIdMapping = refIdMapping;
_bamRealignmentFactory = bamRealignmentFactory;
_dataSourceFactory = dataSourceFactory;
_geminiSampleOptions = geminiSampleOptions;
_realignmentOptions = realignmentOptions;
_geminiFactory = geminiFactory;
_maxDegreeOfParallelism = Math.Min(_stitcherOptions.NumThreads, Environment.ProcessorCount);
}
public GeminiWorkflow(IGeminiDataSourceFactory dataSourceFactory,
IGeminiDataOutputFactory dataOutputFactory, GeminiOptions geminiOptions,
GeminiSampleOptions geminiSampleOptions, RealignmentOptions realignmentOptions, StitcherOptions stitcherOptions, string outputDirectory, RealignmentAssessmentOptions realignmentAssessmentOptions, IndelFilteringOptions indelFilteringOptions, ISamtoolsWrapper samtoolsWrapper)
{
_dataSourceFactory = dataSourceFactory;
_dataOutputFactory = dataOutputFactory;
_geminiOptions = geminiOptions;
_geminiSampleOptions = geminiSampleOptions;
_realignmentOptions = realignmentOptions;
_samtoolsWrapper = samtoolsWrapper;
_stitcherOptions = stitcherOptions ?? new StitcherOptions();
_geminiFactory = new GeminiFactory(geminiOptions, indelFilteringOptions);
var bamRealignmentFactory = new BamRealignmentFactory(geminiOptions,
realignmentAssessmentOptions, stitcherOptions, realignmentOptions,
outputDirectory);
_bamRealignmentFactory = bamRealignmentFactory;
}
private static void Execute(List <BamAlignment> alignments, List <ReadPair> reads, GeminiOptions geminiOptions, StitcherOptions stitcherOptions, List <ReadPair> lonerpairs = null)
{
var mockOutcomesWriter = new Mock <IOutcomesWriter>();
var mockDataOutputFactory = DataflowMocks.MockDataOutputFactory(alignments);
var mockTextWriter = new Mock <ITextWriter>();
mockDataOutputFactory.Setup(x => x.GetTextWriter(It.IsAny <string>()))
.Returns(mockTextWriter.Object);
var mockReader = DataflowMocks.MockReader();
var mockReadPairSource = DataflowMocks.MockDataSource(reads, lonerpairs);
var mockDataSourceFactory = DataflowMocks.MockDataSourceFactory(mockReader, mockReadPairSource);
var mockSamtoolsWrapper = new Mock <ISamtoolsWrapper>();
var geminiSampleOptions = new GeminiSampleOptions()
{
RefId = 1, OutputFolder = "OutFolder"
};
var geminiWorkflow = new GeminiWorkflow(mockDataSourceFactory.Object, mockDataOutputFactory.Object,
geminiOptions, geminiSampleOptions, new RealignmentOptions(), stitcherOptions, "outdir",
new RealignmentAssessmentOptions(), new IndelFilteringOptions(), mockSamtoolsWrapper.Object);
geminiWorkflow.Execute();
}
public BinEvidenceFactory(GeminiOptions geminiOptions, GeminiSampleOptions geminiSampleOptions)
{
_geminiOptions = geminiOptions;
_geminiSampleOptions = geminiSampleOptions;
}
