public void GetGeneSection()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz")), CompressionMode.Decompress);
var indexStream = ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz.jsi"));
var outStream = new MemoryStream();
using (var writer = new StreamWriter(outStream, Encoding.UTF8, 512, true))
using (var qp = new QueryProcessor(new StreamReader(readStream), indexStream, writer))
{
writer.NewLine = "\r\n";
qp.PrintSection("genes");
}
Assert.NotEqual(0, outStream.Length);
outStream.Position = 0;
using (var reader = new StreamReader(outStream))
{
var count = 0;
var line = reader.ReadLine();
while (line != null)
{
count++;
line = reader.ReadLine();
}
Assert.Equal(127, count);
}
}
public void EndOfFile()
{
using (var ms = new MemoryStream())
{
var writeBuffer = ByteUtilities.GetRandomBytes(100);
var readBuffer = new byte[60];
using (var bgzipStream = new BlockGZipStream(ms, CompressionMode.Compress, true))
{
bgzipStream.Write(writeBuffer, 0, writeBuffer.Length);
}
ms.Position = 0;
using (var bgzipStream = new BlockGZipStream(ms, CompressionMode.Decompress))
{
int numBytesRead = bgzipStream.Read(readBuffer, 0, 0);
Assert.Equal(0, numBytesRead);
numBytesRead = bgzipStream.Read(readBuffer, 0, readBuffer.Length);
Assert.Equal(readBuffer.Length, numBytesRead);
numBytesRead = bgzipStream.Read(readBuffer, 0, readBuffer.Length);
Assert.Equal(writeBuffer.Length - readBuffer.Length, numBytesRead);
numBytesRead = bgzipStream.Read(readBuffer, 0, readBuffer.Length);
Assert.Equal(0, numBytesRead);
}
}
}
public void IndexCreation_multiChromosome()
{
var jsonStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress);
var writeStream = new MemoryStream();
using (var indexCreator = new IndexCreator(jsonStream, writeStream))
{
indexCreator.CreateIndex();
}
JasixIndex readBackIndex;
var readStream = new MemoryStream(writeStream.ToArray());
readStream.Seek(0, SeekOrigin.Begin);
using (readStream)
{
readBackIndex = new JasixIndex(readStream);
}
Assert.Equal(2268, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924));
Assert.Equal(14035925971, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096));
Assert.Equal(433156622693, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164));
Assert.Equal(439602269527, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044));
}
private int ReadGeneLines(Stream jsonStream)
{
var lineCount = 0;
using (var bGzipStream = new BlockGZipStream(jsonStream, CompressionMode.Decompress))
using (var reader = new StreamReader(bGzipStream))
{
string line;
while ((line = reader.ReadLine()) != null)
{
if (line == string.Empty)
{
continue;
}
if (line == FooterLine)
{
break;
}
if (!line.EndsWith(','))
{
line += ',';
}
lineCount++;
_geneLines.Add(line);
}
}
return(lineCount);
}
public IndexCreator(BlockGZipStream readStream, Stream writeStream)
{
_reader = new BgzipTextReader(readStream);
_writeStream = writeStream;
_chromBenchmark = new Benchmark();
_benchmark = new Benchmark();
}
private static (Stream jsonStream, Stream jasixStream) GetNirvanaJsonStreamWithoutGenes(int chromNumber)
{
var jsonStream = new MemoryStream();
var jasixStream = new MemoryStream();
using (var bgZipStream = new BlockGZipStream(jsonStream, CompressionMode.Compress, true))
using (var writer = new BgzipTextWriter(bgZipStream))
using (var jasixIndex = new JasixIndex())
{
writer.Write(NirvanaHeader);
writer.Flush();
jasixIndex.BeginSection(JasixCommons.PositionsSectionTag, writer.Position);
for (int i = 100 * chromNumber; i < 123 * chromNumber; i++)
{
writer.WriteLine($"{{\"chromosome\":\"chr{chromNumber}\",\"position\":{i}}},");
if (i % 50 == 0)
{
writer.Flush(); //creating another block
}
}
writer.WriteLine($"{{\"chromosome\":\"chr{chromNumber}\",\"position\":{100 *chromNumber +25}}}");
writer.Flush();
jasixIndex.EndSection(JasixCommons.PositionsSectionTag, writer.Position);
writer.Write(NirvanaFooter);
jasixIndex.Write(jasixStream);
}
jsonStream.Position = 0;
jasixStream.Position = 0;
return(jsonStream, jasixStream);
}
public IndexCreator(BlockGZipStream readStream, Stream writeStream)
{
_reader = new BgzipTextReader(readStream);
_writeStream = writeStream;
_processedChromosome = new HashSet <string>();
_chromBenchmark = new Benchmark();
_benchmark = new Benchmark();
}
public void DoubleDispose()
{
using (var ms = new MemoryStream())
{
var bgzipStream = new BlockGZipStream(ms, CompressionMode.Compress);
bgzipStream.Dispose();
bgzipStream.Dispose();
}
}
public void All_jsons_with_genes()
{
var jsonStreams = new Stream[3];
var jasixSteams = new Stream[3];
(jsonStreams[0], jasixSteams[0]) = GetJsonStreams(ChromosomeUtilities.Chr1, true);
(jsonStreams[1], jasixSteams[1]) = GetJsonStreams(ChromosomeUtilities.Chr2, true);
(jsonStreams[2], jasixSteams[2]) = GetJsonStreams(ChromosomeUtilities.Chr3, true);
var outStream = new MemoryStream();
using (var stitcher = new JsonStitcher(jsonStreams, jasixSteams, outStream, true))
{
stitcher.Stitch();
}
outStream.Position = 0;
var sb = new StringBuilder();
using (var bgZipStream = new BlockGZipStream(outStream, CompressionMode.Decompress))
using (var reader = new StreamReader(bgZipStream))
{
string line;
while ((line = reader.ReadLine()) != null)
{
sb.Append(line + '\n');
}
}
var fullJson = sb.ToString();
//making sure all the first and last positions are present in the merged JSON
Assert.Contains("\"header\":{\"annotator\":\"NirvanaTest\"", fullJson);
Assert.Contains("{\"chromosome\":\"chr1\",\"position\":100}", fullJson);
Assert.Contains("{\"chromosome\":\"chr1\",\"position\":122}", fullJson);
Assert.Contains("{\"chromosome\":\"chr2\",\"position\":200}", fullJson);
Assert.Contains("{\"chromosome\":\"chr2\",\"position\":222}", fullJson);
Assert.Contains("{\"chromosome\":\"chr3\",\"position\":300}", fullJson);
Assert.Contains("{\"chromosome\":\"chr3\",\"position\":322}", fullJson);
//checking if all the genes are there
Assert.Contains("gene1A", fullJson);
Assert.Contains("gene1B", fullJson);
Assert.Contains("gene2A", fullJson);
Assert.Contains("gene2B", fullJson);
Assert.Contains("gene3A", fullJson);
Assert.Contains("gene3B", fullJson);
//need to check if this is a valid json
var jObject = JObject.Parse(fullJson);
Assert.NotNull(jObject);
}
public void BgzipTextWriter_EndToEnd()
{
var asterisks = new string('*', BlockGZipStream.BlockGZipFormatCommon.BlockSize);
var observedLines = new List <string>();
var observedPositions = new List <long>();
using (var ms = new MemoryStream())
{
using (var stream = new BlockGZipStream(ms, CompressionMode.Compress, true))
using (var writer = new BgzipTextWriter(stream))
{
writer.Flush();
writer.WriteLine("BOB");
writer.WriteLine();
writer.Flush();
writer.Write("AB");
writer.Write("");
writer.Write("C");
writer.Write(" ");
writer.WriteLine("123");
writer.WriteLine(asterisks);
writer.WriteLine(asterisks);
writer.WriteLine(asterisks);
}
ms.Position = 0;
using (var reader = new BgzipTextReader(new BlockGZipStream(ms, CompressionMode.Decompress)))
{
while (true)
{
string line = reader.ReadLine();
observedPositions.Add(reader.Position);
if (line == null)
{
break;
}
observedLines.Add(line);
}
}
}
Assert.Equal(6, observedLines.Count);
Assert.Equal("BOB", observedLines[0]);
Assert.Equal(0, observedLines[1].Length);
Assert.Equal("ABC 123", observedLines[2]);
Assert.Equal(asterisks, observedLines[3]);
Assert.Equal(4, observedPositions[0]);
Assert.Equal(5, observedPositions[1]);
Assert.Equal(13, observedPositions[2]);
Assert.Equal(43843598, observedPositions[3]);
Assert.Equal(87097359, observedPositions[4]);
}
private static void WriteGenes(ILogger logger, UgaGene[] genes)
{
logger.Write($"- writing genes to {Path.GetFileName(ExternalFiles.UniversalGeneFilePath)}... ");
using (var stream = new BlockGZipStream(FileUtilities.GetCreateStream(ExternalFiles.UniversalGeneFilePath), CompressionMode.Compress))
using (var writer = new UgaGeneWriter(stream))
{
writer.Write(genes);
}
logger.WriteLine("finished");
}
public static byte[] GetCompressedBlock(string s, int compressionLevel = 1)
{
using (var stream = new MemoryStream())
{
using (var memStream = new BlockGZipStream(stream, CompressionMode.Compress, true))
using (var writer = new StreamWriter(memStream))
{
writer.Write(s);
}
return(stream.ToArray());
}
}
public void FileIO()
{
var observedDecompressedBuffer = new byte[_expectedDecompressedBuffer.Length];
string randomPath = RandomPath.GetRandomPath();
// compress the data
long observedPosition;
using (var writer = new BlockGZipStream(FileUtilities.GetCreateStream(randomPath), CompressionMode.Compress))
{
writer.Write(_expectedDecompressedBuffer, 0, _expectedDecompressedBuffer.Length);
observedPosition = writer.Position;
var exception = Record.Exception(() =>
{
var buffer = new byte[10];
// ReSharper disable once AccessToDisposedClosure
writer.Read(buffer, 0, 1);
});
Assert.NotNull(exception);
Assert.IsType <CompressionException>(exception);
}
const long expectedPosition = 979042574;
Assert.Equal(expectedPosition, observedPosition);
// decompress the data
using (var reader = new BlockGZipStream(FileUtilities.GetReadStream(randomPath), CompressionMode.Decompress))
{
reader.Read(observedDecompressedBuffer, 0, _expectedDecompressedBuffer.Length);
var exception = Record.Exception(() =>
{
var buffer = new byte[10];
// ReSharper disable once AccessToDisposedClosure
reader.Write(buffer, 0, 1);
});
Assert.NotNull(exception);
Assert.IsType <CompressionException>(exception);
}
Assert.Equal(_expectedDecompressedBuffer, observedDecompressedBuffer);
}
public void StreamIO()
{
byte[] observedCompressedBuffer;
var observedDecompressedBuffer = new byte[_expectedDecompressedBuffer.Length];
using (var ms = new MemoryStream())
{
// compress the data
using (var writer = new BlockGZipStream(ms, CompressionMode.Compress, true, 9))
{
Assert.Throws <CompressionException>(delegate
{
// ReSharper disable once AccessToDisposedClosure
writer.Read(observedDecompressedBuffer, 0, 1);
});
Assert.True(writer.CanWrite);
Assert.False(writer.CanRead);
Assert.False(writer.CanSeek);
writer.Write(_expectedDecompressedBuffer, 0, _expectedDecompressedBuffer.Length);
}
observedCompressedBuffer = ms.ToArray();
ms.Seek(0, SeekOrigin.Begin);
// decompress the data
using (var reader = new BlockGZipStream(ms, CompressionMode.Decompress))
{
Assert.Throws <CompressionException>(delegate
{
// ReSharper disable once AccessToDisposedClosure
reader.Write(_expectedDecompressedBuffer, 0, 1);
});
Assert.False(reader.CanWrite);
Assert.True(reader.CanRead);
Assert.True(reader.CanSeek);
reader.Read(observedDecompressedBuffer, 0, _expectedDecompressedBuffer.Length);
}
}
Assert.Equal(_expectedDecompressedBuffer, observedDecompressedBuffer);
Assert.Equal(9629, observedCompressedBuffer.Length);
}
public void WritingTask()
{
using (FileStream stream = new FileStream(options.ResultFileName, FileMode.Create))
{
using (BlockGZipStream compressingStream = new BlockGZipStream(stream, BlockGZipStreamMode.Compressing))
{
while (true)
{
var block = writingQueue.Dequeue();
if (block == stopWorkingTask)
{
break;
}
compressingStream.WriteBlock(block);
}
}
}
}
private void ReadingTask()
{
using (Stream fileStream = new FileStream(options.SourceFileName, FileMode.Open, FileAccess.Read))
{
using (BlockGZipStream gzipStream = new BlockGZipStream(fileStream, BlockGZipStreamMode.Decompressing))
{
for (int i = 0; i < gzipStream.Lenght; i++)
{
readingQueue.Enqueue(gzipStream.ReadBlock(i));
}
}
}
for (int i = 0; i < options.ThreadsCount; i++)
{
readingQueue.Enqueue(stopWorkingTask);
}
}
public void NotImplementedMethods()
{
using (var ms = new MemoryStream())
{
// ReSharper disable AccessToDisposedClosure
using (var writer = new BlockGZipStream(ms, CompressionMode.Compress, true))
{
Assert.Throws <NotSupportedException>(delegate
{
// ReSharper disable once UnusedVariable
long len = writer.Length;
});
Assert.Throws <NotSupportedException>(delegate { writer.SetLength(10); });
Assert.Throws <NotSupportedException>(delegate { writer.Seek(0, SeekOrigin.Begin); });
}
// ReSharper restore AccessToDisposedClosure
}
}
private static AnnotationPosition[] AdjustPartitionGenomicStarts(IReadOnlyList <long> blockBasedOffsets, string vcfUrl,
IIntervalForest <IGene> geneIntervalForest, IDictionary <string, IChromosome> refNameToChromosome)
{
var allAdjustedStarts = new AnnotationPosition[blockBasedOffsets.Count];
for (var index = 0; index < blockBasedOffsets.Count; index++)
{
long blockBasedOffset = blockBasedOffsets[index];
using (var stream = PersistentStreamUtils.GetReadStream(vcfUrl, blockBasedOffset))
using (var gzipStream = new BlockGZipStream(stream, CompressionMode.Decompress))
{
var annotationPosition = GetFirstGenomicPosition(gzipStream, index == 0);
allAdjustedStarts[index] = FindProperStartPosition(annotationPosition, geneIntervalForest, refNameToChromosome);
}
}
AnnotationPosition[] adjustedStarts = MergeConsecutiveEqualValues(allAdjustedStarts).ToArray();
return(adjustedStarts);
}
public void ReadBlockCorrupted()
{
using (var ms = new MemoryStream())
using (var truncatedMs = new MemoryStream())
using (var corruptMs = new MemoryStream())
{
using (var bgzipStream = new BlockGZipStream(ms, CompressionMode.Compress, true))
using (var writer = new StreamWriter(bgzipStream, Encoding.ASCII, 4096))
{
writer.WriteLine("The quick brown fox jumped over the lazy dog.");
}
var compressedData = ms.ToArray();
truncatedMs.Write(compressedData, 0, compressedData.Length - 10);
truncatedMs.Position = 0;
corruptMs.Write(compressedData, 0, BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength);
var randomBytes = BlockStreamTests.GetRandomBytes(500);
corruptMs.Write(randomBytes, 0, randomBytes.Length);
corruptMs.Position = 0;
var readBuffer = new byte[60];
Assert.Throws <CompressionException>(delegate
{
using (var bgzipStream = new BlockGZipStream(truncatedMs, CompressionMode.Decompress))
{
bgzipStream.Read(readBuffer, 0, readBuffer.Length);
}
});
Assert.Throws <CompressionException>(delegate
{
using (var bgzipStream = new BlockGZipStream(corruptMs, CompressionMode.Decompress))
{
bgzipStream.Read(readBuffer, 0, readBuffer.Length);
}
});
}
}
public void GetHeaderOnly()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz")), CompressionMode.Decompress);
var indexStream = ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz.jsi"));
var outStream = new MemoryStream();
using (var writer = new StreamWriter(outStream, Encoding.UTF8, 512, true))
using (var qp = new QueryProcessor(new StreamReader(readStream), indexStream, writer))
{
qp.PrintHeaderOnly();
}
Assert.NotEqual(0, outStream.Length);
outStream.Position = 0;
using (var reader = new StreamReader(outStream))
{
string headerLine = reader.ReadToEnd();
Assert.Equal("{\"header\":{\"annotator\":\"Nirvana 2.0.9.0\",\"creationTime\":\"2018-04-30 17:17:23\",\"genomeAssembly\":\"GRCh37\",\"schemaVersion\":6,\"dataVersion\":\"91.26.45\",\"dataSources\":[{\"name\":\"VEP\",\"version\":\"91\",\"description\":\"Ensembl\",\"releaseDate\":\"2018-03-05\"},{\"name\":\"ClinVar\",\"version\":\"20180129\",\"description\":\"A freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence\",\"releaseDate\":\"2018-01-29\"},{\"name\":\"COSMIC\",\"version\":\"84\",\"description\":\"somatic mutation and related details and information relating to human cancers\",\"releaseDate\":\"2018-02-13\"},{\"name\":\"dbSNP\",\"version\":\"150\",\"description\":\"Identifiers for observed variants\",\"releaseDate\":\"2017-04-03\"},{\"name\":\"gnomAD_exome\",\"version\":\"2.0.2\",\"description\":\"Exome allele frequencies from Genome Aggregation Database (gnomAD)\",\"releaseDate\":\"2017-10-05\"},{\"name\":\"gnomAD\",\"version\":\"2.0.2\",\"description\":\"Whole genome allele frequencies from Genome Aggregation Database (gnomAD)\",\"releaseDate\":\"2017-10-05\"},{\"name\":\"MITOMAP\",\"version\":\"20180228\",\"description\":\"Small variants in the MITOMAP human mitochondrial genome database\",\"releaseDate\":\"2018-02-28\"},{\"name\":\"1000 Genomes Project\",\"version\":\"Phase 3 v5a\",\"description\":\"A public catalogue of human variation and genotype data\",\"releaseDate\":\"2013-05-27\"},{\"name\":\"TOPMed\",\"version\":\"freeze_5\",\"description\":\"Allele frequencies from TOPMed data lifted over using dbSNP ids.\",\"releaseDate\":\"2017-08-28\"},{\"name\":\"ClinGen\",\"version\":\"20160414\",\"releaseDate\":\"2016-04-14\"},{\"name\":\"DGV\",\"version\":\"20160515\",\"description\":\"Provides a comprehensive summary of structural variation in the human genome\",\"releaseDate\":\"2016-05-15\"},{\"name\":\"MITOMAP\",\"version\":\"20180228\",\"description\":\"Large structural variants in the MITOMAP human mitochondrial genome database\",\"releaseDate\":\"2018-02-28\"},{\"name\":\"ExAC\",\"version\":\"0.3.1\",\"description\":\"Gene scores from the ExAC project\",\"releaseDate\":\"2016-03-16\"},{\"name\":\"OMIM\",\"version\":\"20180213\",\"description\":\"An Online Catalog of Human Genes and Genetic Disorders\",\"releaseDate\":\"2018-02-13\"},{\"name\":\"phyloP\",\"version\":\"hg19\",\"description\":\"46 way conservation score between humans and 45 other vertebrates\",\"releaseDate\":\"2009-11-10\"}]}}\r\n", headerLine);
}
}
public void GetChromosomeList()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz")), CompressionMode.Decompress);
var indexStream = ResourceUtilities.GetReadStream(Resources.TopPath("Clinvar20150901.json.gz.jsi"));
var outStream = new MemoryStream();
using (var writer = new StreamWriter(outStream, Encoding.UTF8, 512, true))
using (var qp = new QueryProcessor(new StreamReader(readStream), indexStream, writer))
{
qp.PrintChromosomeList();
}
Assert.NotEqual(0, outStream.Length);
outStream.Position = 0;
using (var reader = new StreamReader(outStream))
{
string chromList = reader.ReadToEnd();
Assert.Equal("1\r\n2\r\n3\r\n4\r\n5\r\n6\r\n7\r\n8\r\n9\r\n10\r\n11\r\n12\r\n13\r\n14\r\n15\r\n16\r\n17\r\n18\r\n19\r\n20\r\n21\r\nX\r\nY\r\n", chromList);
}
}
private static Stream GetAppropriateStream(Stream stream, CompressionAlgorithm compressionAlgorithm)
{
Stream newStream;
switch (compressionAlgorithm)
{
case CompressionAlgorithm.BlockGZip:
newStream = new BlockGZipStream(stream, CompressionMode.Decompress);
break;
case CompressionAlgorithm.GZip:
newStream = new GZipStream(stream, CompressionMode.Decompress);
break;
default:
newStream = stream;
break;
}
return(newStream);
}
private void WriteGeneBlocks(Stream stream)
{
using (var bGzipStream = new BlockGZipStream(stream, CompressionMode.Compress, _leaveOutStreamOpen))
using (var writer = new StreamWriter(bGzipStream))
{
var count = _geneLines.Count;
if (count == 0)
{
writer.WriteLine(FooterLine);
return;
}
writer.WriteLine(GeneHeaderLine);
var i = 0;
foreach (var geneLine in _geneLines.OrderBy(x => x))
{
i++;
//the last gene line shouldn't have a comma at the end
writer.WriteLine(i == count ? geneLine.TrimEnd(',') : geneLine);
}
writer.WriteLine(FooterLine);
}
}
private static Stream GetAppropriateStream(Stream stream, CompressionAlgorithm compressionAlgorithm)
{
Stream newStream;
// ReSharper disable once SwitchStatementMissingSomeCases
switch (compressionAlgorithm)
{
case CompressionAlgorithm.BlockGZip:
newStream = new BlockGZipStream(stream, CompressionMode.Decompress);
break;
case CompressionAlgorithm.GZip:
newStream = new GZipStream(stream, CompressionMode.Decompress);
break;
default:
newStream = stream;
break;
}
return(newStream);
}
private void ConfigureResourceUtilizationOptions()
{
availableRamBytes = availableRamBytes / 2;
if (CommandName == "compress")
{
ReadingBlockSizeBytes = availableRamBytes / ThreadsCount;
int maxBlockSizeBytes = 1 * 1024 * 1024;
ReadingBlockSizeBytes = ReadingBlockSizeBytes > maxBlockSizeBytes ? maxBlockSizeBytes : ReadingBlockSizeBytes;
}
else
{
using (Stream fileStream = new FileStream(SourceFileName, FileMode.Open, FileAccess.Read))
{
using (BlockGZipStream gzipStream = new BlockGZipStream(fileStream, BlockGZipStreamMode.Decompressing))
{
ReadingBlockSizeBytes = gzipStream.GetMaxStoredBlockSizeBytes();
}
}
}
if (availableRamBytes < ReadingBlockSizeBytes)
{
BadOption("source-filename", "Sorry. You don't have enough ram.");
}
if (availableRamBytes / ReadingBlockSizeBytes < ThreadsCount)
{
ThreadsCount = availableRamBytes / ReadingBlockSizeBytes;
}
var taskByThread = availableRamBytes / ReadingBlockSizeBytes / ThreadsCount;
if (taskByThread > TasksByTreadByDefault)
{
taskByThread = TasksByTreadByDefault;
}
TaskCount = taskByThread * ThreadsCount;
}
public void TestIndexCreation()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress);
var tempFile = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
using (var indexCreator = new IndexCreator(readStream, FileUtilities.GetCreateStream(tempFile)))
{
indexCreator.CreateIndex();
}
JasixIndex readBackIndex;
using (var stream = FileUtilities.GetReadStream(tempFile))
{
readBackIndex = new JasixIndex(stream);
}
Assert.Equal(1591, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924));
Assert.Equal(11500956299, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096));
Assert.Equal(372100991296, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164));
Assert.Equal(377682846863, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044));
File.Delete(tempFile);
}
public void InvalidHeader()
{
const string dummyString = "The quick brown fox jumped over the lazy dog.";
using (var ms = new MemoryStream())
using (var truncatedMs = new MemoryStream())
{
using (var writer = new StreamWriter(ms, Encoding.ASCII, 4096, true))
{
writer.WriteLine(dummyString);
}
var observedCompressedBuffer = ms.ToArray();
truncatedMs.Write(ms.ToArray(), 0, 17);
ms.Seek(0, SeekOrigin.Begin);
truncatedMs.Seek(0, SeekOrigin.Begin);
// attempt to decompress the data
Assert.Throws <CompressionException>(delegate
{
using (var reader = new BlockGZipStream(ms, CompressionMode.Decompress, true))
{
reader.Read(observedCompressedBuffer, 0, observedCompressedBuffer.Length);
}
});
Assert.Throws <CompressionException>(delegate
{
using (var reader = new BlockGZipStream(truncatedMs, CompressionMode.Decompress, true))
{
reader.Read(observedCompressedBuffer, 0, observedCompressedBuffer.Length);
}
});
}
}
// 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));
}
}
