public void VirtualPosition_LoopBack()
{
const long expectedVirtualPosition = 3591443256775;
(long fileOffset, int blockOffset) = VirtualPosition.From(expectedVirtualPosition);
long observedVirtualPosition = VirtualPosition.To(fileOffset, blockOffset);
Assert.Equal(expectedVirtualPosition, observedVirtualPosition);
}
// ReSharper disable once UnusedMember.Global
public AnnotationResult Run(AnnotationConfig config, ILambdaContext context)
{
var result = new AnnotationResult {
id = config.id
};
string snsTopicArn = null;
var runLog = new StringBuilder();
try
{
LogUtilities.UpdateLogger(context.Logger, runLog);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
LambdaUtilities.DeleteTempOutput();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
string vcfUrl = config.vcfUrl;
using (var annotationResources = GetAnnotationResources(config))
{
if (annotationResources.InputStartVirtualPosition == -1)
{
return(GetSuccessOutput(result));
}
long fileOffset = VirtualPosition.From(annotationResources.InputStartVirtualPosition).FileOffset;
using (var preloadVcfStream = PersistentStreamUtils.GetReadStream(vcfUrl, fileOffset))
{
annotationResources.GetVariantPositions(new BlockGZipStream(preloadVcfStream, CompressionMode.Decompress), config.annotationRange.ToGenomicRange(annotationResources.SequenceProvider.RefNameToChromosome));
}
Logger.WriteLine("Scan for positions to preload complete.");
using (var aes = new AesCryptoServiceProvider())
{
FileMetadata jsonMetadata, jasixMetadata;
string jsonPath = Path.GetTempPath() + LambdaUrlHelper.JsonSuffix;
string jasixPath = jsonPath + LambdaUrlHelper.JsonIndexSuffix;
using (var inputVcfStream = new BlockGZipStream(PersistentStreamUtils.GetReadStream(vcfUrl, fileOffset), CompressionMode.Decompress))
using (var headerStream = config.annotationRange == null ? null : new BlockGZipStream(PersistentStreamUtils.GetReadStream(vcfUrl), CompressionMode.Decompress))
//
using (var jsonFileStream = FileUtilities.GetCreateStream(jsonPath))
using (var jsonCryptoStream = new CryptoStream(jsonFileStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var jsonMd5Stream = new MD5Stream(jsonCryptoStream))
//
using (var jasixFileStream = FileUtilities.GetCreateStream(jasixPath))
using (var jasixCryptoStream = new CryptoStream(jasixFileStream, aes.CreateEncryptor(), CryptoStreamMode.Write))
using (var jasixMd5Stream = new MD5Stream(jasixCryptoStream))
{
IVcfFilter vcfFilter = config.annotationRange == null
? new NullVcfFilter() as IVcfFilter
: new VcfFilter(config.annotationRange.ToGenomicRange(annotationResources.SequenceProvider.RefNameToChromosome));
using (var jsonCompressStream = new BlockGZipStream(jsonMd5Stream, CompressionMode.Compress))
{
StreamAnnotation.Annotate(headerStream, inputVcfStream, jsonCompressStream, jasixMd5Stream, annotationResources, vcfFilter, true);
}
Logger.WriteLine("Annotation done.");
jsonMetadata = jsonMd5Stream.GetFileMetadata();
jasixMetadata = jasixMd5Stream.GetFileMetadata();
}
result.filePath = S3Utilities.GetKey(config.outputDir.path, config.outputPrefix + LambdaUrlHelper.JsonSuffix);
string jasixKey = result.filePath + LambdaUrlHelper.JsonIndexSuffix;
var s3Client = config.outputDir.GetS3Client(context.RemainingTime);
s3Client.DecryptUpload(config.outputDir.bucketName, jasixKey, jasixPath, aes, jasixMetadata);
s3Client.DecryptUpload(config.outputDir.bucketName, result.filePath, jsonPath, aes, jsonMetadata);
Logger.WriteLine("Nirvana result files uploaded.");
}
}
LambdaUtilities.DeleteTempOutput();
if (string.IsNullOrEmpty(result.filePath))
{
throw new FileNotFoundException();
}
return(GetSuccessOutput(result));
}
catch (Exception exception)
{
LambdaUtilities.DeleteTempOutput();
return(HandleException(runLog, result, exception, snsTopicArn));
}
}
private static long[] GetAllLinearFileOffsets(Tabix.Index tabixIndex) => MergeConsecutiveEqualValues(tabixIndex.ReferenceSequences.SelectMany(x => x.LinearFileOffsets.Select(y => VirtualPosition.From((long)y).FileOffset))).ToArray();
