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 AnnotationResources GetAnnotationResources()
{
var annotationResources = new AnnotationResources(_refSequencePath, _inputCachePrefix, SupplementaryAnnotationDirectories, null, _pluginDirectory, _disableRecomposition, _forceMitochondrialAnnotation);
if (SupplementaryAnnotationDirectories.Count == 0)
{
return(annotationResources);
}
using (var preloadVcfStream = GZipUtilities.GetAppropriateStream(
new PersistentStream(PersistentStreamUtils.GetReadStream(_vcfPath),
ConnectUtilities.GetFileConnectFunc(_vcfPath), 0)))
{
annotationResources.GetVariantPositions(preloadVcfStream, null);
}
return(annotationResources);
}
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);
}
