private static void ValidateVepVersion(this SingleConfig config)
{
if (config.vepVersion == 0)
{
config.vepVersion = CacheUtilities.DefaultVepVersion;
}
if (CacheUtilities.IsVepVersionSupported(config.vepVersion))
{
return;
}
throw new UserErrorException($"An invalid VEP version ({config.vepVersion}) was specified. Please choose one of the following versions: {CacheUtilities.GetSupportedVersions()}");
}
private static AnnotationResources GetAnnotationResources(SingleConfig lambdaConfig)
{
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(lambdaConfig.genomeAssembly);
string cachePathPrefix = CacheUtilities.GetCachePathPrefix(lambdaConfig.vepVersion, genomeAssembly);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
string annotatorVersion = "Nirvana " + CommandLineUtilities.GetVersion(Assembly.GetAssembly(typeof(SingleAnnotationLambda)));
var metrics = new PerformanceMetrics();
Logger.WriteLine($"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);
}
