public static RealignmentAssessmentOptions DeepCopy(this RealignmentAssessmentOptions options)
{
return(new RealignmentAssessmentOptions
{
CheckSoftclipsForMismatches = options.CheckSoftclipsForMismatches,
TrackActualMismatches = options.TrackActualMismatches
});
}
public GeminiApplicationOptions()
{
StitcherOptions = new StitcherOptions();
GeminiSampleOptions = new GeminiSampleOptions();
IndelFilteringOptions = new IndelFilteringOptions();
RealignmentAssessmentOptions = new RealignmentAssessmentOptions();
RealignmentOptions = new RealignmentOptions();
GeminiOptions = new GeminiOptions();
}
public BamRealignmentFactory(GeminiOptions geminiOptions,
RealignmentAssessmentOptions realignmentAssessmentOptions, StitcherOptions stitcherOptions, RealignmentOptions realignmentOptions, string outputDir)
{
_geminiOptions = geminiOptions;
_realignmentAssessmentOptions = realignmentAssessmentOptions;
_stitcherOptions = stitcherOptions;
_realignmentOptions = realignmentOptions;
_outputDir = outputDir;
}
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;
}
