public AnnotationResources(string refSequencePath, string inputCachePrefix, List <string> saDirectoryPaths, List <SaUrls> customAnnotations, string pluginDirectory, bool disableRecomposition, bool forceMitochondrialAnnotation)
{
SequenceProvider = ProviderUtilities.GetSequenceProvider(refSequencePath);
var annotationFiles = new AnnotationFiles();
saDirectoryPaths?.ForEach(x => annotationFiles.AddFiles(x));
customAnnotations?.ForEach(x => annotationFiles.AddFiles(x));
TranscriptAnnotationProvider = ProviderUtilities.GetTranscriptAnnotationProvider(inputCachePrefix, SequenceProvider);
SaProvider = ProviderUtilities.GetNsaProvider(annotationFiles);
ConservationProvider = ProviderUtilities.GetConservationProvider(annotationFiles);
RefMinorProvider = ProviderUtilities.GetRefMinorProvider(annotationFiles);
GeneAnnotationProvider = ProviderUtilities.GetGeneAnnotationProvider(annotationFiles);
Plugins = PluginUtilities.LoadPlugins(pluginDirectory);
Annotator = ProviderUtilities.GetAnnotator(TranscriptAnnotationProvider, SequenceProvider, SaProvider,
ConservationProvider, GeneAnnotationProvider, Plugins);
Recomposer = disableRecomposition
? new NullRecomposer()
: Phantom.Recomposer.Recomposer.Create(SequenceProvider, TranscriptAnnotationProvider);
DataSourceVersions = GetDataSourceVersions(Plugins, TranscriptAnnotationProvider, SaProvider,
GeneAnnotationProvider, ConservationProvider).ToList();
VepDataVersion = TranscriptAnnotationProvider.VepVersion + "." + CacheConstants.DataVersion + "." +
SaCommon.DataVersion;
ForceMitochondrialAnnotation = forceMitochondrialAnnotation;
}
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;
}