public GeminiApplicationOptions()
{
StitcherOptions = new StitcherOptions();
GeminiSampleOptions = new GeminiSampleOptions();
IndelFilteringOptions = new IndelFilteringOptions();
RealignmentAssessmentOptions = new RealignmentAssessmentOptions();
RealignmentOptions = new RealignmentOptions();
GeminiOptions = new GeminiOptions();
}
public static IndelFilteringOptions DeepCopy(this IndelFilteringOptions options)
{
return(new IndelFilteringOptions
{
FoundThreshold = options.FoundThreshold,
MinAnchor = options.MinAnchor,
BinSize = options.BinSize,
StrictFoundThreshold = options.StrictFoundThreshold,
StrictAnchorThreshold = options.StrictAnchorThreshold,
MaxMess = options.MaxMess,
});
}
public GeminiFactory(GeminiOptions geminiOptions, IndelFilteringOptions indelFilteringOptions)
{
_geminiOptions = geminiOptions;
_indelFilteringOptions = indelFilteringOptions;
}
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;
}
