private static ExitCodes ProgramExecution()
{
var logger = new ConsoleLogger();
var bundle = DataBundle.GetDataBundle(_inputReferencePath, _inputPrefix);
int numRefSeqs = bundle.SequenceReader.NumRefSeqs;
var chromosome = ReferenceNameUtilities.GetChromosome(bundle.SequenceReader.RefNameToChromosome, _referenceName);
bundle.Load(chromosome);
string outputStub = GetOutputStub(chromosome, bundle.Source);
var interval = new ChromosomeInterval(chromosome, _referencePosition, _referenceEndPosition);
var transcripts = GetTranscripts(logger, bundle, interval);
var sift = GetPredictionStaging(logger, "SIFT", transcripts, chromosome, bundle.SiftPredictions, bundle.SiftReader, x => x.SiftIndex, numRefSeqs);
var polyphen = GetPredictionStaging(logger, "PolyPhen", transcripts, chromosome, bundle.PolyPhenPredictions, bundle.PolyPhenReader, x => x.PolyPhenIndex, numRefSeqs);
string referenceBases = GetReferenceBases(logger, bundle.SequenceReader, interval);
var regulatoryRegionIntervalArrays = GetRegulatoryRegionIntervalArrays(logger, bundle.TranscriptCache, interval, numRefSeqs);
var transcriptIntervalArrays = PredictionUtilities.UpdateTranscripts(transcripts, bundle.SiftPredictions,
sift.Predictions, bundle.PolyPhenPredictions, polyphen.Predictions, numRefSeqs);
var transcriptStaging = GetTranscriptStaging(bundle.TranscriptCacheData.Header, transcriptIntervalArrays, regulatoryRegionIntervalArrays);
WriteCache(logger, FileUtilities.GetCreateStream(CacheConstants.TranscriptPath(outputStub)), transcriptStaging, "transcript");
WriteCache(logger, FileUtilities.GetCreateStream(CacheConstants.SiftPath(outputStub)), sift.Staging, "SIFT");
WriteCache(logger, FileUtilities.GetCreateStream(CacheConstants.PolyPhenPath(outputStub)), polyphen.Staging, "PolyPhen");
WriteReference(logger, CacheConstants.BasesPath(outputStub), bundle.SequenceReader, chromosome,
referenceBases, interval.Start);
return(ExitCodes.Success);
}