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/"));
}