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;
}
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);
}