private static AnnotationResources GetAnnotationResources(AnnotationConfig annotationConfig)
{
var genomeAssembly = GenomeAssemblyHelper.Convert(annotationConfig.genomeAssembly);
string cachePathPrefix = LambdaUrlHelper.GetCacheFolder().UrlCombine(genomeAssembly.ToString()).UrlCombine(LambdaUrlHelper.DefaultCacheSource);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
string saManifestUrl = LambdaUtilities.GetManifestUrl(annotationConfig.supplementaryAnnotations ?? "latest", genomeAssembly);
var metrics = new PerformanceMetrics();
var annotationResources = new AnnotationResources(nirvanaS3Ref, cachePathPrefix,
saManifestUrl == null? null: new List <string> {
saManifestUrl
},
annotationConfig.customAnnotations,
annotationConfig.customStrUrl,
false,
false,
false,
metrics);
using (var tabixStream = PersistentStreamUtils.GetReadStream(annotationConfig.tabixUrl))
{
annotationResources.InputStartVirtualPosition = GetTabixVirtualPosition(annotationConfig.annotationRange, tabixStream, annotationResources.SequenceProvider.RefNameToChromosome);
}
Logger.WriteLine($"Tabix position :{annotationResources.InputStartVirtualPosition}");
return(annotationResources);
}
// ReSharper disable once UnusedMember.Global
public Stream Run(SingleConfig config, ILambdaContext context)
{
string snsTopicArn = null;
Stream response;
try
{
LogUtilities.UpdateLogger(context.Logger, null);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
config.Validate();
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(config.genomeAssembly);
var cacheConfiguration = new CacheConfiguration(genomeAssembly, config.supplementaryAnnotations, config.vepVersion);
bool preloadRequired = !string.IsNullOrEmpty(config.supplementaryAnnotations);
AnnotationResources annotationResources = GetAndCacheAnnotationResources(config, cacheConfiguration);
if (genomeAssembly != GenomeAssembly.hg19)
{
annotationResources.Annotator.EnableMitochondrialAnnotation();
}
(IPosition position, string[] sampleNames) = config.GetPositionAndSampleNames(annotationResources.SequenceProvider, annotationResources.RefMinorProvider);
if (position.Chromosome.IsEmpty())
{
throw new UserErrorException($"An unknown chromosome was specified ({config.variant.chromosome})");
}
string annotationResult = GetPositionAnnotation(position, annotationResources, sampleNames, preloadRequired);
response = SingleResult.Create(config.id, LambdaUrlHelper.SuccessMessage, annotationResult);
}
catch (Exception exception)
{
response = ExceptionHandler.GetStream(config.id, snsTopicArn, exception);
}
return(response);
}
private static AnnotationResources GetAnnotationResources(SingleConfig lambdaConfig)
{
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(lambdaConfig.genomeAssembly);
string cachePathPrefix = CacheUtilities.GetCachePathPrefix(lambdaConfig.vepVersion, genomeAssembly);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
string annotatorVersion = "Nirvana " + CommandLineUtilities.GetVersion(Assembly.GetAssembly(typeof(SingleAnnotationLambda)));
var metrics = new PerformanceMetrics();
Logger.WriteLine($"Cache prefix: {cachePathPrefix}");
//todo: get customStrTsv from lambdaConfig
var annotationResources = new AnnotationResources(nirvanaS3Ref, cachePathPrefix,
null, lambdaConfig.customAnnotations, null, false, false, false, metrics)
{
AnnotatorVersionTag = annotatorVersion
};
return(annotationResources);
}
