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);
}
public void Dispose()
{
SequenceProvider?.Dispose();
TranscriptAnnotationProvider?.Dispose();
SaProvider?.Dispose();
ConservationProvider?.Dispose();
RefMinorProvider?.Dispose();
GeneAnnotationProvider?.Dispose();
}
public static ITranscriptAnnotationProvider GetTranscriptAnnotationProvider(string path,
ISequenceProvider sequenceProvider)
{
var benchmark = new Benchmark();
var provider = new TranscriptAnnotationProvider(path, sequenceProvider);
var wallTimeSpan = benchmark.GetElapsedTime();
Console.WriteLine("Cache Time: {0} ms", wallTimeSpan.TotalMilliseconds);
return(provider);
}
