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;
}
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);
}