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);
}
