private static IEnumerable <AnnotationRange> GetAnnotationRanges(NirvanaConfig config, GenomeAssembly genomeAssembly)
{
string cachePathPrefix = LambdaUtilities.GetCachePathPrefix(genomeAssembly);
IntervalForest <IGene> geneIntervalForest;
IDictionary <string, IChromosome> refNameToChromosome;
List <long> blockOffsets;
using (var tabixStream = PersistentStreamUtils.GetReadStream(config.tabixUrl))
using (var tabixReader = new BinaryReader(new BlockGZipStream(tabixStream, CompressionMode.Decompress)))
using (var referenceStream = PersistentStreamUtils.GetReadStream(LambdaUrlHelper.GetRefUrl(genomeAssembly)))
using (var sequenceProvider = new ReferenceSequenceProvider(referenceStream))
using (var taProvider = new TranscriptAnnotationProvider(cachePathPrefix, sequenceProvider, null))
{
long vcfSize = HttpUtilities.GetLength(config.vcfUrl);
int numPartitions = Math.Max(Math.Min((int)((vcfSize - 1) / MinPartitionSize + 1), MaxNumPartitions), MinNumPartitions);
var tabixIndex = Reader.Read(tabixReader, sequenceProvider.RefNameToChromosome);
blockOffsets = PartitionUtilities.GetFileOffsets(config.vcfUrl, numPartitions, tabixIndex);
IntervalArray <ITranscript>[] transcriptIntervalArrays = taProvider.TranscriptIntervalArrays;
geneIntervalForest = GeneForestGenerator.GetGeneForest(transcriptIntervalArrays);
refNameToChromosome = sequenceProvider.RefNameToChromosome;
}
IEnumerable <AnnotationRange> annotationRanges = PartitionUtilities.GenerateAnnotationRanges(blockOffsets, config.vcfUrl, geneIntervalForest, refNameToChromosome);
return(annotationRanges);
}
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($"Tabix position :{annotationResources.InputStartVirtualPosition}");
return(annotationResources);
}
public ValidationResult Run(ValidationConfig config, ILambdaContext context)
{
string snsTopicArn = null;
try
{
LogUtilities.UpdateLogger(context.Logger, null);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
config.Validate();
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(config.genomeAssembly);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
var refProvider = ProviderUtilities.GetSequenceProvider(nirvanaS3Ref);
using (var stream = PersistentStreamUtils.GetReadStream(config.customStrUrl))
TryLoadStrFile(stream, genomeAssembly, refProvider);
}
catch (Exception exception)
{
return(HandleException(config.id, exception, snsTopicArn));
}
return(GetSuccessOutput(config.id));
}
private static AnnotationResources GetAnnotationResources(SingleConfig lambdaConfig)
{
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(lambdaConfig.genomeAssembly);
string cachePathPrefix = CacheUtilities.GetCachePathPrefix(lambdaConfig.vepVersion, genomeAssembly);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
string annotatorVersion = "Nirvana " + CommandLineUtilities.GetVersion(Assembly.GetAssembly(typeof(SingleAnnotationLambda)));
var metrics = new PerformanceMetrics();
Logger.WriteLine($"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);
}
public void GetS3RefLocation_AsExpected()
{
Assert.Equal(LambdaUrlHelper.GetRefPrefix("whatever") + "GRCh37" + LambdaUrlHelper.RefSuffix, LambdaUrlHelper.GetRefUrl(GenomeAssembly.GRCh37, "whatever"));
}
private static VariantAnnotationsParser GetVariantAnnotationsParserFromCustomTsvStream(PersistentStream customTsvStream)
{
var parser = VariantAnnotationsParser.Create(new StreamReader(GZipUtilities.GetAppropriateStream(customTsvStream)));
parser.SequenceProvider = new ReferenceSequenceProvider(PersistentStreamUtils.GetReadStream(LambdaUrlHelper.GetRefUrl(parser.Assembly)));
return(parser);
}