public BamRealignmentFactory(GeminiOptions geminiOptions,
RealignmentAssessmentOptions realignmentAssessmentOptions, StitcherOptions stitcherOptions, RealignmentOptions realignmentOptions, string outputDir)
{
_geminiOptions = geminiOptions;
_realignmentAssessmentOptions = realignmentAssessmentOptions;
_stitcherOptions = stitcherOptions;
_realignmentOptions = realignmentOptions;
_outputDir = outputDir;
}
public GeminiApplicationOptions()
{
StitcherOptions = new StitcherOptions();
GeminiSampleOptions = new GeminiSampleOptions();
IndelFilteringOptions = new IndelFilteringOptions();
RealignmentAssessmentOptions = new RealignmentAssessmentOptions();
RealignmentOptions = new RealignmentOptions();
GeminiOptions = new GeminiOptions();
}
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 static RealignmentOptions DeepCopy(this RealignmentOptions options)
{
return(new RealignmentOptions()
{
CategoriesForRealignment = options.CategoriesForRealignment,
CategoriesForSnowballing = options.CategoriesForSnowballing,
MaskPartialInsertion = options.MaskPartialInsertion,
MaxIndelSize = options.MaxIndelSize,
MinimumUnanchoredInsertionLength = options.MinimumUnanchoredInsertionLength,
NumSubSamplesForSnowballing = options.NumSubSamplesForSnowballing,
PairAwareEverything = options.PairAwareEverything,
RemaskMessySoftclips = options.RemaskMessySoftclips
});
}
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;
}
public AggregateRegionProcessor(ChrReference chrReference, Dictionary <int, string> refIdMapping,
BamRealignmentFactory bamRealignmentFactory, GeminiOptions geminiOptions, IGeminiFactory geminiFactory,
string chrom, IGeminiDataSourceFactory dataSourceFactory, RealignmentOptions realignmentOptions,
ConcurrentDictionary <string, IndelEvidence> masterIndelLookup,
ConcurrentDictionary <HashableIndel, int[]> masterOutcomesLookup,
ConcurrentDictionary <HashableIndel, int> masterFinalIndels, List <PairClassification> categoriesForRealignment, ConcurrentDictionary <string, int> progressTracker)
{
_chrReference = chrReference;
_refIdMapping = refIdMapping;
_bamRealignmentFactory = bamRealignmentFactory;
_geminiOptions = geminiOptions;
_geminiFactory = geminiFactory;
_chrom = chrom;
_dataSourceFactory = dataSourceFactory;
_realignmentOptions = realignmentOptions;
_masterIndelLookup = masterIndelLookup;
_masterOutcomesLookup = masterOutcomesLookup;
_masterFinalIndels = masterFinalIndels;
_categoriesForRealignment = categoriesForRealignment;
_progressTracker = progressTracker;
}
