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($"Tabix position :{annotationResources.InputStartVirtualPosition}"); return(annotationResources); }
public void GetDataUrlBase_AsExpected() { Assert.Equal($"http://somewhere.on.the.earth/ab0cf104f39708eabd07b8cb67e149ba-Cache/{CacheConstants.DataVersion}/", LambdaUrlHelper.GetCacheFolder("http://somewhere.on.the.earth/")); Assert.Equal($"http://somewhere.on.the.earth/d95867deadfe690e40f42068d6b59df8-References/{ReferenceSequenceCommon.HeaderVersion}/Homo_sapiens.", LambdaUrlHelper.GetRefPrefix("http://somewhere.on.the.earth/")); }
public static string GetCachePathPrefix(GenomeAssembly genomeAssembly, string baseUrl = null) { return(LambdaUrlHelper.GetCacheFolder(baseUrl).UrlCombine(genomeAssembly.ToString()) .UrlCombine(LambdaUrlHelper.DefaultCacheSource)); }
public void GetDataUrlBase_AsExpected() { Assert.Equal("http://somewhere.on.the.earth/ab0cf104f39708eabd07b8cb67e149ba-Cache/26/", LambdaUrlHelper.GetCacheFolder("http://somewhere.on.the.earth/")); Assert.Equal("http://somewhere.on.the.earth/d95867deadfe690e40f42068d6b59df8-References/7/Homo_sapiens.", LambdaUrlHelper.GetRefPrefix("http://somewhere.on.the.earth/")); }