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);
}
/// <summary>
/// updates a transcript
/// mini-cache filename example: ENST00000255416_chr1_Ensembl79.ndb
/// </summary>
public UpdateStatus Update(DataBundle bundle, string outputCacheDir, ushort desiredVepVersion, List <string> outputFiles)
{
var transcript = MiniCacheUtilities.GetDesiredTranscript(bundle, _transcriptId, RefIndex);
if (transcript == null)
{
return(UpdateStatus.IdNotFound);
}
var packets = new List <TranscriptPacket> {
new TranscriptPacket(transcript)
};
foreach (var packet in packets)
{
bundle.Load(packet.ReferenceIndex);
packet.SiftPrediction = packet.Transcript.SiftIndex == -1
? null
: bundle.SiftCache.Predictions[packet.Transcript.SiftIndex];
packet.PolyPhenPrediction = packet.Transcript.PolyPhenIndex == -1
? null
: bundle.PolyPhenCache.Predictions[packet.Transcript.PolyPhenIndex];
}
var numRefSeqs = bundle.Sequence.Renamer.NumRefSeqs;
var sift = PredictionUtilities.GetStaging(bundle, true, packets, numRefSeqs);
var polyphen = PredictionUtilities.GetStaging(bundle, false, packets, numRefSeqs);
PredictionUtilities.FixIndices(packets);
var outputCache = MiniCacheUtilities.CreateCache(bundle.Cache.Header, packets);
var outputStub = GetOutputStub(outputCacheDir, _transcriptId,
bundle.Sequence.Renamer.UcscReferenceNames[transcript.ReferenceIndex], TranscriptDataSource,
desiredVepVersion);
MiniCacheUtilities.WriteTranscriptCache(outputCache, outputStub, outputFiles);
MiniCacheUtilities.WritePredictionCaches(sift, polyphen, outputStub, outputFiles);
MiniCacheUtilities.WriteBases(bundle, packets, outputStub, outputFiles);
return(UpdateStatus.Current);
}
/// <summary>
/// updates a position
/// mini-cache filename example: chr1_713044_755966_RefSeq79_pos.ndb
/// </summary>
public UpdateStatus Update(DataBundle bundle, string outputCacheDir, ushort desiredVepVersion, List <string> outputFiles)
{
bundle.Load(RefIndex);
string vcfLine = $"{bundle.Sequence.Renamer.UcscReferenceNames[RefIndex]}\t{_position}\t.\tC\t<CN0>\t100\tPASS\tEND={_endPosition};SVTYPE=CNV";
var transcripts = MiniCacheUtilities.GetTranscriptsByVcf(bundle, vcfLine);
if (transcripts == null)
{
return(UpdateStatus.IdNotFound);
}
var packets = transcripts.Select(transcript => new TranscriptPacket(transcript)).ToList();
foreach (var packet in packets)
{
bundle.Load(packet.ReferenceIndex);
packet.SiftPrediction = packet.Transcript.SiftIndex == -1
? null
: bundle.SiftCache.Predictions[packet.Transcript.SiftIndex];
packet.PolyPhenPrediction = packet.Transcript.PolyPhenIndex == -1
? null
: bundle.PolyPhenCache.Predictions[packet.Transcript.PolyPhenIndex];
}
var numRefSeqs = bundle.Sequence.Renamer.NumRefSeqs;
var sift = PredictionUtilities.GetStaging(bundle, true, packets, numRefSeqs);
var polyphen = PredictionUtilities.GetStaging(bundle, false, packets, numRefSeqs);
PredictionUtilities.FixIndices(packets);
var outputCache = MiniCacheUtilities.CreateCache(bundle.Cache.Header, packets);
var outputStub = GetOutputStub(outputCacheDir, bundle.Sequence.Renamer.UcscReferenceNames[RefIndex],
_position, _endPosition, TranscriptDataSource, desiredVepVersion);
MiniCacheUtilities.WriteTranscriptCache(outputCache, outputStub, outputFiles);
MiniCacheUtilities.WritePredictionCaches(sift, polyphen, outputStub, outputFiles);
MiniCacheUtilities.WriteBases(bundle, packets, outputStub, outputFiles);
return(UpdateStatus.Current);
}
public IHttpActionResult MakePrediction(string id)
{
PredictionUtilities.MakePredictions(this.repository, id);
return(Ok());
}
