/// <summary>
/// Allows the game to perform any initialization it needs to before starting to run.
/// This is where it can query for any required services and load any non-graphic
/// related content. Calling base.Initialize will enumerate through any components
/// and initialize them as well.
/// </summary>
protected override void Initialize()
{
#if DEBUG
this.Window.Title = "Asteroids-dev-debug";
#else
this.Window.Title = "Asteroids-dev-release";
#endif
this.Window.Title += " - Version: " + this.GetVersionString();
System.Diagnostics.Trace.WriteLine(DateTime.Now + " " + this.Window.Title);
UserConfig.Instance = UserConfig.Load();
WindowSettings.Initialize(this, this.graphics);
WindowSettings.SetWindowResolution(new Point(UserConfig.Instance.ScreenWidth, UserConfig.Instance.ScreenHeight));
WindowSettings.SetBorderless(UserConfig.Instance.Borderless);
WindowSettings.MinWindowResolution = GameConfig.MinWindowSize;
WindowSettings.UnitsVisible = new Vector2(1280, 720);
this.renderTarget = new RenderTarget2D(this.GraphicsDevice, WindowSettings.RenderArea.Width, WindowSettings.RenderArea.Height);
this.sceneManager = new GUISceneManager(this);
this.Components.Add(new Kadro.Input.KeyboardInput(this));
this.Components.Add(new MouseInput(this));
this.Components.Add(new GamepadInput(this));
this.Components.Add(new TouchpanelInput(this));
this.performanceCounter = new PerformanceMetrics();
Assets.Initialize(Content);
this.networkManager = new NetworkManager(UserConfig.Instance.NetworkName);
this.connectionInfo = new BaseConnection();
base.Initialize();
}
private static AnnotationResources GetAnnotationResources(AnnotationConfig annotationConfig)
{
var genomeAssembly = GenomeAssemblyHelper.Convert(annotationConfig.genomeAssembly);
string cachePathPrefix = LambdaUrlHelper.GetCacheFolder().UrlCombine(genomeAssembly.ToString()).UrlCombine(LambdaUrlHelper.DefaultCacheSource);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
string saManifestUrl = LambdaUtilities.GetManifestUrl(annotationConfig.supplementaryAnnotations ?? "latest", genomeAssembly);
var metrics = new PerformanceMetrics();
var annotationResources = new AnnotationResources(nirvanaS3Ref, cachePathPrefix,
saManifestUrl == null? null: new List <string> {
saManifestUrl
},
annotationConfig.customAnnotations,
annotationConfig.customStrUrl,
false,
false,
false,
metrics);
using (var tabixStream = PersistentStreamUtils.GetReadStream(annotationConfig.tabixUrl))
{
annotationResources.InputStartVirtualPosition = GetTabixVirtualPosition(annotationConfig.annotationRange, tabixStream, annotationResources.SequenceProvider.RefNameToChromosome);
}
Logger.WriteLine($"Tabix position :{annotationResources.InputStartVirtualPosition}");
return(annotationResources);
}
public void AccountTime(
StatementMetricHandle metricsHandle,
PerformanceMetrics performanceMetrics,
int numInputEvents)
{
stmtMetricRepository.AccountTimes(metricsHandle, performanceMetrics, numInputEvents);
}
public void AddMetrics(PerformanceMetrics performanceMetrics)
{
lock (this) {
_performanceMetrics.UserTime += performanceMetrics.UserTime;
_performanceMetrics.PrivTime += performanceMetrics.PrivTime;
_performanceMetrics.TotalTime += performanceMetrics.TotalTime;
}
}
public void QueueYouTubeChecks()
{
_youtubeTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.YouTube;
metrics.ScheduledInterval = _botSettings.IntervalSettings.YouTubeLive;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogYouTubeGaming("Checking YouTube Gaming Channels.");
await _platformServices.CheckYouTubeLive();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogYouTubeGaming("YouTube Gaming Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.YouTubeLive);
_youtubePublishedTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.YouTube;
metrics.ScheduledInterval = _botSettings.IntervalSettings.YouTubePublished;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogYouTube("Checking YouTube Published");
await _platformServices.CheckPublishedYouTube();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogYouTube("YouTube Published Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.YouTubePublished);
_youtubePublishedOwnerTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = true;
metrics.Platform = Constants.YouTube;
metrics.ScheduledInterval = _botSettings.IntervalSettings.YouTubePublished;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogYouTube("Checking Owner YouTube Published");
await _platformServices.CheckOwnerPublishedYouTube();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogYouTube("Owner YouTube Published Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.YouTubePublished);
}
public static ExitCodes Annotate(Stream headerStream, Stream inputVcfStream, Stream outputJsonStream,
Stream outputJsonIndexStream, AnnotationResources annotationResources, IVcfFilter vcfFilter, bool ignoreEmptyChromosome = false)
{
var logger = outputJsonStream is BlockGZipStream ? new ConsoleLogger() : (ILogger) new NullLogger();
var metrics = new PerformanceMetrics(logger);
using (annotationResources)
using (var vcfReader = GetVcfReader(headerStream, inputVcfStream, annotationResources, vcfFilter))
using (var jsonWriter = new JsonWriter(outputJsonStream, outputJsonIndexStream, annotationResources, Date.CurrentTimeStamp, vcfReader.GetSampleNames(), false))
{
try
{
CheckGenomeAssembly(annotationResources, vcfReader);
SetMitochondrialAnnotationBehavior(annotationResources, vcfReader);
int previousChromIndex = -1;
IPosition position;
while ((position = vcfReader.GetNextPosition()) != null)
{
if (ignoreEmptyChromosome && position.Chromosome.IsEmpty())
{
continue;
}
if (previousChromIndex != position.Chromosome.Index)
{
annotationResources.PreLoad(position.Chromosome);
}
previousChromIndex = UpdatePerformanceMetrics(previousChromIndex, position.Chromosome, metrics);
var annotatedPosition = position.Variants != null?annotationResources.Annotator.Annotate(position) : null;
string json = annotatedPosition?.GetJsonString();
if (json != null)
{
jsonWriter.WriteJsonEntry(annotatedPosition.Position, json);
}
metrics.Increment();
}
jsonWriter.WriteAnnotatedGenes(annotationResources.Annotator.GetGeneAnnotations());
}
catch (Exception e)
{
e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine;
throw;
}
}
metrics.ShowAnnotationTime();
return(ExitCodes.Success);
}
private static int UpdatePerformanceMetrics(int previousChromIndex, IChromosome chromosome,
PerformanceMetrics metrics)
{
// ReSharper disable once InvertIf
if (chromosome.Index != previousChromIndex)
{
metrics.StartAnnotatingReference(chromosome);
previousChromIndex = chromosome.Index;
}
return(previousChromIndex);
}
/// <summary>
/// Account statement times.
/// </summary>
/// <param name="handle">statement handle</param>
/// <param name="performanceMetrics">performance metrics</param>
/// <param name="numInput">number of input rows</param>
public void AccountTimes(
StatementMetricHandle handle,
PerformanceMetrics performanceMetrics,
int numInput)
{
var array = groupMetrics[handle.GroupNum];
using (array.RWLock.AcquireReadLock()) {
var metric = array.GetAddMetric(handle.Index);
metric.AddMetrics(performanceMetrics);
metric.AddNumInput(numInput);
}
}
public AnnotationResources(string refSequencePath, string inputCachePrefix, List <string> saDirectoryPaths, List <SaUrls> customAnnotations,
string customStrTsvPath, bool disableRecomposition, bool forceMitochondrialAnnotation, bool useLegacyVids, PerformanceMetrics metrics)
{
Metrics = metrics;
PerformanceMetrics.ShowInitializationHeader();
SequenceProvider = ProviderUtilities.GetSequenceProvider(refSequencePath);
var annotationFiles = new AnnotationFiles();
saDirectoryPaths?.ForEach(x => annotationFiles.AddFiles(x));
customAnnotations?.ForEach(x => annotationFiles.AddFiles(x));
ProteinConservationProvider = ProviderUtilities.GetProteinConservationProvider(annotationFiles);
ProteinConservationProvider?.Load();
metrics.Cache.Start();
TranscriptAnnotationProvider = ProviderUtilities.GetTranscriptAnnotationProvider(inputCachePrefix, SequenceProvider, ProteinConservationProvider);
metrics.ShowCacheLoad();
SaProvider = ProviderUtilities.GetNsaProvider(annotationFiles);
ConservationProvider = ProviderUtilities.GetConservationProvider(annotationFiles);
LcrProvider = ProviderUtilities.GetLcrProvider(annotationFiles);
RefMinorProvider = ProviderUtilities.GetRefMinorProvider(annotationFiles);
GeneAnnotationProvider = ProviderUtilities.GetGeneAnnotationProvider(annotationFiles);
IRepeatExpansionProvider repeatExpansionProvider = GetRepeatExpansionProvider(SequenceProvider.Assembly,
SequenceProvider.RefNameToChromosome, SequenceProvider.RefIndexToChromosome.Count, customStrTsvPath);
MitoHeteroplasmyProvider = MitoHeteroplasmyReader.GetProvider();
Annotator = new Annotator(TranscriptAnnotationProvider, SequenceProvider, SaProvider, ConservationProvider, LcrProvider, GeneAnnotationProvider,
repeatExpansionProvider);
if (useLegacyVids)
{
VidCreator = new LegacyVariantId(SequenceProvider.RefNameToChromosome);
}
else
{
VidCreator = new VariantId();
}
Recomposer = disableRecomposition
? new NullRecomposer()
: Phantom.Recomposer.Recomposer.Create(SequenceProvider, TranscriptAnnotationProvider, VidCreator);
DataSourceVersions = GetDataSourceVersions(TranscriptAnnotationProvider, SaProvider, GeneAnnotationProvider, ConservationProvider, LcrProvider, MitoHeteroplasmyProvider)
.ToList();
VepDataVersion = TranscriptAnnotationProvider.VepVersion + "." + CacheConstants.DataVersion + "." + SaCommon.DataVersion;
ForceMitochondrialAnnotation = forceMitochondrialAnnotation;
}
} //network is training indicator
public Network()
{
Ip = null;
Lr = null;
Filename = "";
//subscribe to configuration data changed
NetConfigData.DataItemChanged += NetConfigDataChanged;
Metrics = new PerformanceMetrics();
TrainRequest = false;
TrainingInProgress = false;
}
/// <summary>
/// Initializes a new instance of the <see cref="StatementMetric"/> class.
/// </summary>
/// <param name="runtimeURI">The runtime URI.</param>
/// <param name="deploymentId">The deployment identifier.</param>
/// <param name="statementName">Name of the statement.</param>
public StatementMetric(
string runtimeURI,
string deploymentId,
string statementName)
: base(runtimeURI)
{
DeploymentId = deploymentId;
StatementName = statementName;
_performanceMetrics = default(PerformanceMetrics);
_numOutputIStream = 0L;
_numOutputRStream = 0L;
_numInput = 0L;
}
/// <summary>
/// constructor
/// </summary>
public PianoAnnotationSource(Stream transcriptCacheStream, CompressedSequenceReader compressedSequenceReader)
{
OverlappingTranscripts = new List <Transcript>();
_performanceMetrics = PerformanceMetrics.Instance;
_compressedSequence = new CompressedSequence();
_dataFileManager = new DataFileManager(compressedSequenceReader, _compressedSequence);
_dataFileManager.Changed += LoadData;
_renamer = _compressedSequence.Renamer;
_aminoAcids = new AminoAcids();
_vid = new VID();
LoadTranscriptCache(transcriptCacheStream, _renamer.NumRefSeqs, out _transcriptIntervalForest);
}
public Network(string filename)
: this()
{
Filename = filename;
Trainer = new Trainer(Filename);
CreateLayers();
ConnectLayers();
Metrics = new PerformanceMetrics();
Trainer.NextCase(Ip, 0);
ScreenUpdateData.DataChanged();
}
//string MyConnection2 = "";
//string MyConnection2 = "";
public async Task LogPerformance(PerformanceMetrics metrics)
{
//var Query = "INSERT INTO `PerformanceLog`(`Platform`, `IsOwner`, `RunTime`, `ScheduledInterval`, `CreatedDate`) " +
// "VALUES('" + metrics.Platform + "'," + metrics.IsOwner + "," + metrics.RunTime + "," +
// metrics.ScheduledInterval + ",'" + metrics.CreatedDate.ToString("yyyy-MM-dd HH:mm:ss") + "')";
//MySqlConnection MyConn2 = new MySqlConnection(MyConnection2);
//MySqlCommand MyCommand2 = new MySqlCommand(Query, MyConn2);
//MySqlDataReader MyReader2;
//MyConn2.Open();
//MyReader2 = MyCommand2.ExecuteReader();
//while (MyReader2.Read())
//{
//}
//MyConn2.Close();
//await MyConn2.ClearPoolAsync(MyConn2);
//await MyConn2.ClearAllPoolsAsync();
}
private static AnnotationResources GetAnnotationResources(SingleConfig lambdaConfig)
{
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(lambdaConfig.genomeAssembly);
string cachePathPrefix = CacheUtilities.GetCachePathPrefix(lambdaConfig.vepVersion, genomeAssembly);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
string annotatorVersion = "Nirvana " + CommandLineUtilities.GetVersion(Assembly.GetAssembly(typeof(SingleAnnotationLambda)));
var metrics = new PerformanceMetrics();
Logger.WriteLine($"Cache prefix: {cachePathPrefix}");
//todo: get customStrTsv from lambdaConfig
var annotationResources = new AnnotationResources(nirvanaS3Ref, cachePathPrefix,
null, lambdaConfig.customAnnotations, null, false, false, false, metrics)
{
AnnotatorVersionTag = annotatorVersion
};
return(annotationResources);
}
public void QueueTwitchServerCheck()
{
_twitchServerTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.Twitch + " - Discover";
metrics.ScheduledInterval = _botSettings.IntervalSettings.TwitchServer;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogTwitch("Checking Twitch Server Channels.");
await _platformServices.CheckTwitchServer();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogTwitch("Twitch Server Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.TwitchServer);
}
public void QueueHealthChecks()
{
_guildCheckTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = true;
metrics.Platform = "Bot - Guild Configuration";
metrics.ScheduledInterval = 60000;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogInfo("Checking Guild Configurations.");
_guildServices.CheckGuildConfigurations();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogInfo("Guild Configuration Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, 600000);
}
public void QueuePicartoChecks()
{
_picartoTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.Picarto;
metrics.ScheduledInterval = _botSettings.IntervalSettings.Picarto;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogPicarto("Checking Picarto Channels.");
await _platformServices.CheckPicartoLive();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogPicarto("Picarto Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.Picarto);
_picartoOwnerTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = true;
metrics.Platform = Constants.Picarto;
metrics.ScheduledInterval = _botSettings.IntervalSettings.Picarto;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogPicarto("Checking Picarto Smashcast Channels.");
await _platformServices.CheckOwnerPicartoLive();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogPicarto("Owner Picarto Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.Picarto);
}
public void QueueVidMeChecks()
{
_vidMeTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.VidMe;
metrics.ScheduledInterval = _botSettings.IntervalSettings.VidMe;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogVidMe("Checking VidMe");
await _platformServices.CheckVidMe();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogVidMe("VidMe Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.VidMe);
_vidMeOwnerTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = true;
metrics.Platform = Constants.VidMe;
metrics.ScheduledInterval = _botSettings.IntervalSettings.VidMe;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogVidMe("Checking Owner VidMe Published");
await _platformServices.CheckOwnerVidMe();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogVidMe("Owner VidMe Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.VidMe);
}
public override void OnEndOfAlgorithm()
{
try
{
GenerateTradeSummary(TradeBuilder.ClosedTrades, "Trade Summary (All Trades)");
GenerateTradeSummary(TradeBuilder.ClosedTrades.Where((t) => t.Direction == TradeDirection.Long), "Trade Summary (Long Trades)");
GenerateTradeSummary(TradeBuilder.ClosedTrades.Where((t) => t.Direction == TradeDirection.Short), "Trade Summary (Short Trades)");
var equityChangePerDay = PerformanceMetrics.EquityChangePerDay(TradeBuilder.ClosedTrades);
var backtestPeriod = EndDate - StartDate;
var TRASYCODRAVOPFACOM = PerformanceMetrics.TRASYCODRAVOPFACOM(TradeBuilder.ClosedTrades, backtestPeriod);
var lakeRatio = PerformanceMetrics.LakeRatio(TradeBuilder.ClosedTrades);
var blissFunction = PerformanceMetrics.BlissFunction(TradeBuilder.ClosedTrades);
Console.WriteLine("TRASYCODRAVOPFACOM: {0} Lake Ratio: {1} Bliss Function: {2}", TRASYCODRAVOPFACOM, lakeRatio, blissFunction);
}
catch (Exception ex)
{
Console.WriteLine(ex);
}
}
private static AnnotationResources GetAnnotationResources()
{
if (_outputFileName == "-")
{
Logger.Silence();
}
var metrics = new PerformanceMetrics();
var annotationResources = new AnnotationResources(_refSequencePath, _inputCachePrefix,
SupplementaryAnnotationDirectories, null, _customStrTsv,
_disableRecomposition, _forceMitochondrialAnnotation, _useLegacyVids, metrics);
if (SupplementaryAnnotationDirectories.Count == 0)
{
return(annotationResources);
}
using (var preloadVcfStream = GZipUtilities.GetAppropriateStream(PersistentStreamUtils.GetReadStream(_vcfPath)))
{
annotationResources.GetVariantPositions(preloadVcfStream, null);
}
return(annotationResources);
}
public static ExitCodes Annotate(Stream headerStream, Stream inputVcfStream, Stream outputJsonStream,
Stream outputJsonIndexStream, AnnotationResources annotationResources, IVcfFilter vcfFilter,
bool ignoreEmptyChromosome)
{
var metrics = annotationResources.Metrics;
PerformanceMetrics.ShowAnnotationHeader();
IChromosome currentChromosome = new EmptyChromosome("dummy");
int numVariants = 0;
IMitoHeteroplasmyProvider mitoHeteroplasmyProvider = MitoHeteroplasmyReader.GetProvider();
using (var vcfReader = GetVcfReader(headerStream, inputVcfStream, annotationResources, vcfFilter, mitoHeteroplasmyProvider))
using (var jsonWriter = new JsonWriter(outputJsonStream, outputJsonIndexStream, annotationResources, Date.CurrentTimeStamp, vcfReader.GetSampleNames(), false))
{
try
{
CheckGenomeAssembly(annotationResources, vcfReader);
SetMitochondrialAnnotationBehavior(annotationResources, vcfReader);
IPosition position;
while ((position = vcfReader.GetNextPosition()) != null)
{
IChromosome chromosome = position.Chromosome;
if (ignoreEmptyChromosome && chromosome.IsEmpty())
{
continue;
}
if (chromosome.Index != currentChromosome.Index)
{
if (!currentChromosome.IsEmpty())
{
metrics.ShowAnnotationEntry(currentChromosome, numVariants);
}
numVariants = 0;
metrics.Preload.Start();
annotationResources.PreLoad(chromosome);
metrics.Preload.Stop();
metrics.Annotation.Start();
currentChromosome = chromosome;
}
var annotatedPosition = position.Variants != null?annotationResources.Annotator.Annotate(position) : null;
string json = annotatedPosition?.GetJsonString();
if (json != null)
{
jsonWriter.WritePosition(annotatedPosition.Position, json);
}
numVariants++;
}
jsonWriter.WriteGenes(annotationResources.Annotator.GetGeneAnnotations());
}
catch (Exception e)
{
e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine;
throw;
}
}
if (!currentChromosome.IsEmpty())
{
metrics.ShowAnnotationEntry(currentChromosome, numVariants);
}
metrics.ShowSummaryTable();
return(ExitCodes.Success);
}
private ExitCodes ProgramExecution()
{
var sequenceProvider = ProviderUtilities.GetSequenceProvider(_refSequencePath);
var transcriptAnnotationProvider = ProviderUtilities.GetTranscriptAnnotationProvider(_inputCachePrefix, sequenceProvider);
var saProvider = ProviderUtilities.GetSaProvider(SupplementaryAnnotationDirectories);
var conservationProvider = ProviderUtilities.GetConservationProvider(SupplementaryAnnotationDirectories);
var refMinorProvider = ProviderUtilities.GetRefMinorProvider(SupplementaryAnnotationDirectories);
var geneAnnotationProvider = ProviderUtilities.GetGeneAnnotationProvider(SupplementaryAnnotationDirectories);
var plugins = PluginUtilities.LoadPlugins(_pluginDirectory);
var annotator = ProviderUtilities.GetAnnotator(transcriptAnnotationProvider, sequenceProvider, saProvider, conservationProvider, geneAnnotationProvider, plugins);
var recomposer = _disableRecomposition ? new NullRecomposer() : Recomposer.Create(sequenceProvider, _inputCachePrefix);
var logger = _outputFileName == "-" ? (ILogger) new NullLogger() : new ConsoleLogger();
var metrics = new PerformanceMetrics(logger);
var dataSourceVersions = GetDataSourceVersions(plugins, transcriptAnnotationProvider, saProvider,
geneAnnotationProvider, conservationProvider);
var vepDataVersion = transcriptAnnotationProvider.VepVersion + "." + CacheConstants.DataVersion + "." + SaDataBaseCommon.DataVersion;
var jasixFileName = _outputFileName + ".json.gz" + JasixCommons.FileExt;
using (var outputWriter = ReadWriteUtilities.GetOutputWriter(_outputFileName))
using (var vcfReader = ReadWriteUtilities.GetVcfReader(_vcfPath, sequenceProvider.RefNameToChromosome, refMinorProvider, _reportAllSvOverlappingTranscripts, recomposer))
using (var jsonWriter = new JsonWriter(outputWriter, _annotatorVersionTag, Date.CurrentTimeStamp, vepDataVersion, dataSourceVersions, sequenceProvider.GenomeAssembly.ToString(), vcfReader.GetSampleNames()))
using (var vcfWriter = _vcf ? new LiteVcfWriter(ReadWriteUtilities.GetVcfOutputWriter(_outputFileName), vcfReader.GetHeaderLines(), _annotatorVersionTag, vepDataVersion, dataSourceVersions) : null)
using (var gvcfWriter = _gvcf ? new LiteVcfWriter(ReadWriteUtilities.GetGvcfOutputWriter(_outputFileName), vcfReader.GetHeaderLines(), _annotatorVersionTag, vepDataVersion, dataSourceVersions) : null)
using (var jasixIndexCreator = new OnTheFlyIndexCreator(FileUtilities.GetCreateStream(jasixFileName)))
{
if (!(outputWriter is BgzipTextWriter bgzipTextWriter))
{
throw new NullReferenceException("Unable to create the bgzip text writer.");
}
try
{
jasixIndexCreator.SetHeader(jsonWriter.Header);
if (vcfReader.IsRcrsMitochondrion && annotator.GenomeAssembly == GenomeAssembly.GRCh37 ||
annotator.GenomeAssembly == GenomeAssembly.GRCh38 ||
_forceMitochondrialAnnotation)
{
annotator.EnableMitochondrialAnnotation();
}
int previousChromIndex = -1;
IPosition position;
var sortedVcfChecker = new SortedVcfChecker();
while ((position = vcfReader.GetNextPosition()) != null)
{
sortedVcfChecker.CheckVcfOrder(position.Chromosome.UcscName);
previousChromIndex = UpdatePerformanceMetrics(previousChromIndex, position.Chromosome, metrics);
var annotatedPosition = annotator.Annotate(position);
string json = annotatedPosition.GetJsonString();
if (json != null)
{
WriteOutput(annotatedPosition, bgzipTextWriter.Position, jasixIndexCreator, jsonWriter, vcfWriter, gvcfWriter, json);
}
else
{
gvcfWriter?.Write(string.Join("\t", position.VcfFields));
}
metrics.Increment();
}
WriteGeneAnnotations(annotator.GetAnnotatedGenes(), jsonWriter);
}
catch (Exception e)
{
e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine;
throw;
}
}
metrics.ShowAnnotationTime();
return(ExitCodes.Success);
}
/// <summary>
/// Constructs a new graphics instance with the specified multisampling quality.
/// </summary>
protected GraphicsContext()
{
// Create performance tracking object
Performance = new PerformanceMetrics();
}
public void QueueTwitchChecks()
{
_twitchTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.Twitch;
metrics.ScheduledInterval = _botSettings.IntervalSettings.Twitch;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogTwitch("Checking Twitch Channels.");
await _platformServices.CheckTwitchLive();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogTwitch("Twitch Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
_initialServicesRan = true;
}, null, 0, _botSettings.IntervalSettings.Twitch);
_twitchFeedTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.Twitch + " - Twitch Feed";
metrics.ScheduledInterval = _botSettings.IntervalSettings.TwitchFeed;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogTwitch("Checking Twitch Channel Feeds.");
await _platformServices.CheckTwitchChannelFeeds();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogTwitch("Twitch Channel Feed Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.TwitchFeed);
_twitchOwnerFeedTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = true;
metrics.Platform = Constants.Twitch + " - Twitch Feed";
metrics.ScheduledInterval = _botSettings.IntervalSettings.TwitchFeed;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogTwitch("Checking Owner Twitch Channel Feeds.");
await _platformServices.CheckTwitchOwnerChannelFeeds();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogTwitch("Owner Twitch Channel Feed Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.TwitchFeed);
_twitchTeamTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.Twitch + " - Teams";
metrics.ScheduledInterval = _botSettings.IntervalSettings.Twitch;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogTwitch("Checking Twitch Teams.");
await _platformServices.CheckTwitchTeams();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogTwitch("Checking Twitch Teams Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.Twitch);
_twitchGameTimer = new Timer(async(e) =>
{
var metrics = new PerformanceMetrics();
metrics.CreatedDate = DateTime.UtcNow;
metrics.IsOwner = false;
metrics.Platform = Constants.Twitch + " - Games";
metrics.ScheduledInterval = _botSettings.IntervalSettings.Twitch;
Stopwatch sw = new Stopwatch();
sw.Start();
Logging.LogTwitch("Checking Twitch Games.");
await _platformServices.CheckTwitchGames();
sw.Stop();
metrics.RunTime = sw.ElapsedMilliseconds;
await _loggingManager.LogPerformance(metrics);
Logging.LogTwitch("Checking Twitch Games Check Complete - Elapsed Runtime: " + sw.ElapsedMilliseconds + " milliseconds.");
}, null, 0, _botSettings.IntervalSettings.Twitch);
}
public async Task LogPerformance(PerformanceMetrics metrics)
{
await _loggingDal.LogPerformance(metrics);
}
