public void DifferentTypeException()
{
var customInterval = new VariantAnnotation.DataStructures.CustomInterval("chr1", 100, 200, "WrongType",
null, null);
var randomPath = GetRandomPath();
var dataVersion = new DataSourceVersion("customInterval", "00", DateTime.Now.Ticks);
using (var writer = new CustomIntervalWriter(randomPath, "chr1", _intervalType, dataVersion))
{
// ReSharper disable once AccessToDisposedClosure
var ex = Assert.Throws <Exception>(() => writer.WriteInterval(customInterval));
Assert.Equal($"Unexpected interval in custom interval writer.\nExpected interval type: {_intervalType}, observed interval type: WrongType", ex.Message);
}
}
private static void CreateNsa(string[] exomeFiles, string genomeFile, DataSourceVersion version)
{
Console.WriteLine($"Processing file: {genomeFile}");
var outName = Path.GetFileNameWithoutExtension(genomeFile);
using (var exomeReader = GetExomeReader(exomeFiles, genomeFile))
using (var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_tempDirectory, outName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_tempDirectory, outName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.GnomadTag, true, false, SaCommon.SchemaVersion, false))
using (var reader = GZipUtilities.GetAppropriateStreamReader(genomeFile))
{
var gnomadReader = new GnomadSnvReader(reader, exomeReader, referenceProvider);
var count = nsaWriter.Write(gnomadReader.GetCombinedItems());
Console.WriteLine($"Wrote {count} items to NSA file.");
}
}
private static IEnumerable <IDataSourceVersion> GetDataSourceVersions(CacheHeader header)
{
var dataSourceVersions = new List <IDataSourceVersion>();
if (header == null)
{
return(dataSourceVersions);
}
var customHeader = header.CustomHeader as TranscriptCacheCustomHeader;
var vepVersion = customHeader?.VepVersion;
var dataSourceVersion = new DataSourceVersion("VEP", vepVersion.ToString(), header.CreationTimeTicks, header.TranscriptSource.ToString());
dataSourceVersions.Add(dataSourceVersion);
return(dataSourceVersions);
}
public void Write_clinvar_basic()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
{
using (var extWriter = new ExtendedBinaryWriter(saStream, Encoding.UTF8, true))
using (var indexExtWriter = new ExtendedBinaryWriter(indexStream, Encoding.UTF8, true))
{
var saWriter = new NsaWriter(extWriter, indexExtWriter, version, GetSequenceProvider(), "clinvar", false, true, SaCommon.SchemaVersion, false, true, false, 1024);
saWriter.Write(GetClinvarItems());
}
saStream.Position = 0;
indexStream.Position = 0;
using (var saReader = new NsaReader(saStream, indexStream, 1024))
{
Assert.Equal(GenomeAssembly.GRCh37, saReader.Assembly);
Assert.Equal(version.ToString(), saReader.Version.ToString());
saReader.PreLoad(_chrom1, new List <int> {
100, 101, 106
});
var annotations = saReader.GetAnnotation(100).ToList();
Assert.Equal("T", annotations[0].refAllele);
Assert.Equal("A", annotations[0].altAllele);
Assert.Equal("\"id\":\"RCV0001\",\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"T\",\"altAllele\":\"A\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]", annotations[0].annotation);
annotations = saReader.GetAnnotation(101).ToList();
Assert.Equal("A", annotations[0].refAllele);
Assert.Equal("", annotations[0].altAllele);
Assert.Equal("\"id\":\"RCV00011\",\"variationId\":101,\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"A\",\"altAllele\":\"-\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]", annotations[0].annotation);
saReader.PreLoad(_chrom2, new List <int> {
200, 205
});
var(refAllele, altAllele, annotation) = saReader.GetAnnotation(200).First();
Assert.Equal("G", refAllele);
Assert.Equal("A", altAllele);
Assert.NotNull(annotation);
}
}
}
private static string GetHeader(DataSourceVersion dataSourceVersion, int dataVersion, string assembly, string keyName, ReportFor reportingFor)
{
var sb = StringBuilderCache.Acquire();
sb.Append($"#name={dataSourceVersion.Name}\n");
sb.Append($"#assembly={assembly}\n");
sb.Append($"#version={dataSourceVersion.Version}\n");
sb.Append($"#description={dataSourceVersion.Description}\n");
var releaseDate = new DateTime(dataSourceVersion.ReleaseDateTicks, DateTimeKind.Utc);
sb.Append($"#releaseDate={releaseDate:yyyy-MM-dd}\n");
sb.Append($"#dataVersion={dataVersion}\n");
sb.Append($"#schemaVersion={JsonCommon.SupplementarySchemaVersion}\n");
sb.Append($"#reportFor={reportingFor}\n");
sb.Append($"#keyName={keyName}\n");
sb.Append("#CHROM\tSTART\tEND\tJSON\n");
return(StringBuilderCache.GetStringAndRelease(sb));
}
private static string GetHeader(DataSourceVersion dataSourceVersion, int dataVersion, string assembly, string keyName, bool isArray)
{
var sb = StringBuilderCache.Acquire();
sb.Append($"#name={dataSourceVersion.Name}\n");
sb.Append($"#assembly={assembly}\n");
sb.Append($"#version={dataSourceVersion.Version}\n");
sb.Append($"#description={dataSourceVersion.Description}\n");
var releaseDate = new DateTime(dataSourceVersion.ReleaseDateTicks, DateTimeKind.Utc);
sb.Append($"#releaseDate={releaseDate:yyyy-MM-dd}\n");
sb.Append($"#dataVersion={dataVersion}\n");
sb.Append($"#schemaVersion={SaTsvCommon.SupplementarySchemaVersion}\n");
sb.Append($"#isArray={isArray}\n");
sb.Append($"#keyName={keyName}\n");
sb.Append("#GENESYMBOL\tJSON\n");
return(StringBuilderCache.GetStringAndRelease(sb));
}
public void ReadBackGeneAnnotations()
{
var writeStream = new MemoryStream();
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks);
var ngaWriter = new NgaWriter(writeStream, version, "mimo", SaCommon.SchemaVersion, true);
ngaWriter.Write(GetGeneAnnotations());
var readStream = new MemoryStream(writeStream.ToArray());
using (var ngaReader = new NgaReader(readStream))
{
Assert.Null(ngaReader.GetAnnotation("gene3"));
Assert.Equal("[{\"mimNumber\":123,\"geneName\":\"gene name 1 ('minibrain', Drosophila, homolog of)\",\"description\":\"describing gene 1\\n\\\"some citation\\\"\",\"phenotypes\":[{\"phenotype\":\"disease 1\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"autosomal recessive\"],\"comments\":\"unconfirmed or possibly spurious mapping\"}]}]", ngaReader.GetAnnotation("gene1"));
Assert.Equal("[{\"mimNumber\":124,\"geneName\":\"gene name 2\",\"phenotypes\":[{\"phenotype\":\"disease 2\",\"mapping\":\"chromosome deletion or duplication syndrome\",\"inheritances\":[\"whatever\",\"never-ever\"],\"comments\":\"nondiseases\"}]}]", ngaReader.GetAnnotation("gene2"));
}
ngaWriter.Dispose();
}
private static IEnumerable <IDataSourceVersion> GetDataSourceVersions(CacheHeader header)
{
var dataSourceVersions = new List <IDataSourceVersion>();
if (header == null)
{
return(dataSourceVersions);
}
ushort vepVersion = header.Custom.VepVersion;
// TODO: Embed the data source version in the next cache file format. This hack let's us handle the SARS-CoV-2 genome
DataSourceVersion dataSourceVersion = vepVersion == 0
? new DataSourceVersion("RefSeq", "NC_045512.2", new DateTime(2020, 3, 20, 0, 0, 0, DateTimeKind.Utc).Ticks, "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2)")
: new DataSourceVersion("VEP", vepVersion.ToString(), header.CreationTimeTicks, header.Source.ToString());
dataSourceVersions.Add(dataSourceVersion);
return(dataSourceVersions);
}
public static NsaWriter GetNsaWriter(Stream nsaStream, Stream indexStream, VariantAnnotationsParser parser, string dataVersion, ISequenceProvider referenceProvider, out DataSourceVersion version)
{
dataVersion = string.IsNullOrEmpty(parser.Version) ? dataVersion : parser.Version;
version = new DataSourceVersion(parser.JsonTag, dataVersion, DateTime.Now.Ticks,
parser.DataSourceDescription);
return(new NsaWriter(
nsaStream,
indexStream,
version,
referenceProvider,
parser.JsonTag,
parser.MatchByAllele, // match by allele
parser.IsArray, // is array
SaCommon.SchemaVersion,
false, // is positional
false, // skip incorrect ref base
true // throw error on conflicting entries
));
}
public void AddScoreTest()
{
var randShorts = GetRandShorts();
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
var writer = new ExtendedBinaryWriter(FileUtilities.GetCreateStream(randomPath));
var version = new DataSourceVersion("phylop", "0", DateTime.Now.Ticks, "unit test");
var phylopWriter = new PhylopWriter("chr1", version, GenomeAssembly.Unknown, 100, writer);
foreach (short s in randShorts)
{
phylopWriter.AddScore(s); // artificially forcing the writer to flush at every 100 scores
}
// we should have 41 intervals but note that the last interval is not dumped by AddScore. Therefore, we have 40
Assert.Equal(40, phylopWriter.ChromosomeIntervals.Count);
writer.Dispose();
File.Delete(randomPath);
}
public void LoopBack()
{
var version = new DataSourceVersion("onekgen", "v0.3", DateTime.Now.Ticks);
using (var reader = new RefMinorReader(new StreamReader(GetStream()), GetSequenceProvider()))
using (var stream = new MemoryStream())
using (var indexStream = new MemoryStream())
using (var writer = new RefMinorDbWriter(new ExtendedBinaryWriter(stream), new ExtendedBinaryWriter(indexStream), version, GetSequenceProvider(), SaCommon.SchemaVersion))
{
writer.Write(reader.GetItems());
stream.Position = 0;
indexStream.Position = 0;
using (var dbReader = new RefMinorDbReader(stream, indexStream))
{
Assert.Equal("T", dbReader.GetGlobalMajorAllele(ChromosomeUtilities.Chr1, 15274));
Assert.Null(dbReader.GetGlobalMajorAllele(ChromosomeUtilities.Chr1, 1524));
}
}
}
private static string GetHeader(DataSourceVersion dataSourceVersion, int schemaVersion, string assembly, string jsonKey, string vcfKeys, bool matchByAllele, bool isArray)
{
var sb = StringBuilderCache.Acquire();
sb.Append($"#name={dataSourceVersion.Name}\n");
if (!string.IsNullOrEmpty(assembly))
{
sb.Append($"#assembly={assembly}\n");
}
sb.Append($"#version={dataSourceVersion.Version}\n");
sb.Append($"#description={dataSourceVersion.Description}\n");
var releaseDate = new DateTime(dataSourceVersion.ReleaseDateTicks, DateTimeKind.Utc);
sb.Append($"#releaseDate={releaseDate:yyyy-MM-dd}\n");
sb.Append($"#dataVersion={schemaVersion}\n");
sb.Append($"#schemaVersion={SaTsvCommon.SupplementarySchemaVersion}\n");
sb.Append($"#matchByAllele={matchByAllele}\n");
sb.Append($"#isArray={isArray}\n");
sb.Append($"#jsonKey={jsonKey}\n");
sb.Append($"#vcfKeys={vcfKeys}\n");
sb.Append("#CHROM\tPOS\tREF\tALT\tVCF\tJSON\n");
return(StringBuilderCache.GetStringAndRelease(sb));
}
public void ReadBackGeneAnnotations()
{
NgaReader reader;
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks);
const string jsonKey = "mimo";
const bool isArray = true;
using (var ms = new MemoryStream())
{
using (var writer = new NgaWriter(ms, version, jsonKey, SaCommon.SchemaVersion, isArray, true))
{
writer.Write(GetGeneAnnotations());
}
ms.Position = 0;
reader = NgaReader.Read(ms);
}
Assert.NotNull(reader);
Assert.Null(reader.GetAnnotation("gene3"));
Assert.Equal("[{\"mimNumber\":123,\"geneName\":\"gene name 1 ('minibrain', Drosophila, homolog of)\",\"description\":\"describing gene 1\\n\\\"some citation\\\"\",\"phenotypes\":[{\"phenotype\":\"disease 1\",\"description\":\"This is disease 1\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"autosomal recessive\"],\"comments\":[\"unconfirmed or possibly spurious mapping\"]}]}]", reader.GetAnnotation("gene1"));
Assert.Equal("[{\"mimNumber\":124,\"geneName\":\"gene name 2\",\"phenotypes\":[{\"phenotype\":\"disease 2\",\"description\":\"COVID-19\",\"mapping\":\"chromosome deletion or duplication syndrome\",\"inheritances\":[\"whatever\",\"never-ever\"],\"comments\":[\"nondiseases\"]}]}]", reader.GetAnnotation("gene2"));
}
private void ReadHeader()
{
var header = _reader.ReadString();
if (header != OmimDatabaseCommon.DataHeader)
{
throw new GeneralException("Unrecognized header in OMIM database");
}
var schema = _reader.ReadUInt16();
if (schema != OmimDatabaseCommon.SchemaVersion)
{
throw new GeneralException(
$"Custom interval database schema mismatch. Expected {OmimDatabaseCommon.SchemaVersion}, observed {schema}");
}
_creationTime = _reader.ReadInt64();
DataVersion = new DataSourceVersion(_reader);
CheckGuard();
}
private void LoadHeader()
{
var identifier = _reader.ReadString();
if (identifier != PhylopCommon.Header)
{
throw new InvalidDataException("Unrecognized file header: " + identifier);
}
var schemaVersion = _reader.ReadInt16();
if (schemaVersion != PhylopCommon.SchemaVersion)
{
throw new InvalidDataException("Expected phylop schema version:" + PhylopCommon.SchemaVersion + " observed schema version: " + schemaVersion);
}
var dataVersion = _reader.ReadInt16();
if (dataVersion != PhylopCommon.DataVersion)
{
Console.WriteLine("WARNING: Expected phylop data version:" + PhylopCommon.DataVersion + " observed data version: " + dataVersion);
}
_genomeAssembly = (GenomeAssembly)_reader.ReadByte();
_version = DataSourceVersion.Read(_reader);
// skip the reference name
_reader.ReadString();
_intervalListPosition = _reader.ReadInt64();
CheckGuard();
LoadChromosomeIntervals();
IsInitialized = true;
}
public NgaReader(Stream stream)
{
_nsaStream = stream;
// read the whole file. Currently they are well under 2MB
var compressedBytes = new byte[2 * 1024 * 1024];
var decompressedBytes = new byte[20 * 1024 * 1024];
var compressedSize = _nsaStream.Read(compressedBytes, 0, compressedBytes.Length);
var zstd = new Zstandard();
var decompressedSize = zstd.Decompress(compressedBytes, compressedSize, decompressedBytes, decompressedBytes.Length);
_memStream = new MemoryStream(decompressedBytes, 0, decompressedSize);
_reader = new ExtendedBinaryReader(_memStream);
Version = DataSourceVersion.Read(_reader);
JsonKey = _reader.ReadAsciiString();
_isArray = _reader.ReadBoolean();
ushort schemaVersion = _reader.ReadOptUInt16();
if (schemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"Expected schema version: {SaCommon.SchemaVersion}, observed: {schemaVersion} for {JsonKey}");
}
}
private Stream GetNsiStream()
{
var stream = new MemoryStream();
var version = new DataSourceVersion("test", "June_2020", DateTime.Now.Ticks, "dummy");
using (var writer = new NsiWriter(stream, version, GenomeAssembly.GRCh37, SaCommon.LowComplexityRegionTag,
ReportFor.AllVariants,
SaCommon.NsiSchemaVersion, true))
{
writer.Write(new []
{
new LcrInterval(ChromosomeUtilities.Chr1, 100, 150),
new LcrInterval(ChromosomeUtilities.Chr1, 300, 450),
new LcrInterval(ChromosomeUtilities.Chr1, 600, 650),
new LcrInterval(ChromosomeUtilities.Chr2, 100, 150),
new LcrInterval(ChromosomeUtilities.Chr2, 300, 450),
new LcrInterval(ChromosomeUtilities.Chr2, 600, 650),
});
}
stream.Position = 0;
return(stream);
}
public static NsiWriter GetNsiWriter(Stream nsiStream, DataSourceVersion version, GenomeAssembly assembly, string jsonTag, ReportFor reportFor) => new NsiWriter(nsiStream, version, assembly, jsonTag, reportFor, SaCommon.SchemaVersion);
public static NgaWriter GetNgaWriter(Stream ngaStream, GeneAnnotationsParser parser, string dataVersion)
{
var version = new DataSourceVersion(parser.JsonTag, dataVersion, DateTime.Now.Ticks);
return(new NgaWriter(ngaStream, version, parser.JsonTag, SaCommon.SchemaVersion, false));
}
public ClinvarTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) : this(new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(),
SaTsvCommon.ClinvarSchemaVersion, InterimSaCommon.ClinvarTag, InterimSaCommon.ClinvarVcfTag, false, sequenceProvider, true))
{
Console.WriteLine(version.ToString());
}
public void ReadAndWriteExacWithMultipleAlleles()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var exacVersion = new DataSourceVersion("ExAC", "0.3.1", DateTime.Parse("2016-03-16").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
exacVersion
};
// create our expected supplementary annotations: note AN_adj is modified in this
const string vcfline =
"19 3121452 . TA T,TAA 17262.47 AC_Adj0_Filter AC=6,9;AC_AFR=0,0;AC_AMR=0,0;AC_Adj=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_Het=0,0,0;AC_Hom=0,0;AC_NFE=0,0;AC_OTH=0,0;AC_SAS=0,0;AF=4.587e-03,6.881e-03;AN=1308;AN_AFR=0;AN_AMR=0;AN_Adj=3;AN_EAS=0;AN_FIN=0;AN_NFE=0;AN_OTH=0;AN_SAS=0;BaseQRankSum=0.437;DP=2838";
var sa = new SupplementaryAnnotationPosition(3121453);
var saCreator = new SupplementaryPositionCreator(sa);
var exacReader = new ExacReader(_renamer);
var additionalItems = new List <SupplementaryDataItem>();
foreach (var exacItem in exacReader.ExtractItems(vcfline))
{
var currentItem = exacItem.SetSupplementaryAnnotations(saCreator);
additionalItems.Add(currentItem);
}
var currentSa = new SupplementaryAnnotationPosition(3121453);
var currentSaCreator = new SupplementaryPositionCreator(currentSa);
foreach (var exacItem in additionalItems)
{
exacItem.SetSupplementaryAnnotations(currentSaCreator);
}
// write the supplementary annotation file
using (
var writer = new SupplementaryAnnotationWriter(randomPath, "chr19",
expectedDataSourceVersions))
{
writer.Write(currentSaCreator, currentSa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(3121453) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
// we want to make sure we are reading the values we have written
var expExaciA =
currentSa.AlleleSpecificAnnotations["iA"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(expExaciA);
var obsExaciA =
observedAnnotation1.AlleleSpecificAnnotations["iA"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(obsExaciA);
Assert.Equal(expExaciA.ExacAllAn, obsExaciA.ExacAllAn);
Assert.Equal(expExaciA.ExacCoverage, obsExaciA.ExacCoverage);
Assert.Equal(expExaciA.ExacAllAc, obsExaciA.ExacAllAc);
Assert.NotNull(obsExaciA.ExacAllAc);
Assert.Null(obsExaciA.ExacFinAc);
Assert.Null(obsExaciA.ExacFinAn);
// we want to make sure we are reading the values we have written
var expExac1 =
currentSa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(expExac1);
var obsExac1 =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as
ExacAnnotation;
Assert.NotNull(obsExac1);
Assert.Equal(expExac1.ExacAllAn, obsExac1.ExacAllAn);
Assert.Equal(expExac1.ExacCoverage, obsExac1.ExacCoverage);
Assert.Equal(expExac1.ExacAllAc, obsExac1.ExacAllAc);
Assert.NotNull(obsExac1.ExacAllAc);
Assert.Null(obsExac1.ExacFinAc);
Assert.Null(obsExac1.ExacFinAn);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteWithSuppIntervals()
{
// NIR-1359
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion
};
// This is the case where Nirvana throws an error: Too many bytes in what should have been a 7 bit encoded Int32.
var sa = new SupplementaryAnnotationPosition(5073770);
var saCreator = new SupplementaryPositionCreator(sa);
// adding a supplementary interval
var intValues = new Dictionary <string, int>();
var doubleValues = new Dictionary <string, double>();
var freqValues = new Dictionary <string, double>();
var stringValues = new Dictionary <string, string>();
var boolValues = new List <string>();
var suppInterval = new SupplementaryInterval(5073770, 5073970, "chr1", "<DUP>", VariantType.duplication, "ClinVar", _renamer, intValues,
doubleValues, freqValues, stringValues, boolValues);
suppInterval.AddStringValue("ID", "RandomClin001");
// the above code was unit tested in MergeDbSnpClinVar()
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr9", expectedDataSourceVersions))
{
writer.SetIntervalList(new List <SupplementaryInterval> {
suppInterval
});
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// read the stored intervals
var suppIntervals = reader.GetSupplementaryIntervals(_renamer).ToList();
Assert.Equal(1, suppIntervals.Count);
foreach (var interval in suppIntervals)
{
Assert.Equal(5073770, interval.Start);
Assert.Equal(5073970, interval.End);
Assert.Equal("<DUP>", interval.AlternateAllele);
Assert.Equal("ClinVar", interval.Source);
Assert.Equal("duplication", interval.VariantType.ToString());
foreach (var keyValuePair in interval.StringValues)
{
if (keyValuePair.Key == "ID")
{
Assert.Equal("RandomClin001", keyValuePair.Value);
}
if (keyValuePair.Key == "vid")
{
Assert.Equal("1:5073770:5073970", keyValuePair.Value);
}
}
}
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public SaTsvWriter(string outputDir, DataSourceVersion dataSourceVersion, string assembly, int schemaVersion, string jsonKey, string vcfKeys,
bool isAlleleSpecific, ISequenceProvider sequenceProvider, bool isArray = false) : this(outputDir, dataSourceVersion, assembly, schemaVersion, jsonKey, vcfKeys, isAlleleSpecific, isArray)
{
_sequenceProvider = sequenceProvider;
}
//todo: filter chromIndex=ushort.Max
public NsaWriter(ExtendedBinaryWriter writer, ExtendedBinaryWriter indexWriter, DataSourceVersion version, ISequenceProvider refProvider, string jsonKey, bool matchByAllele, bool isArray, int schemaVersion, bool isPositional, bool skipIncorrectRefEntries = true, bool throwErrorOnConflicts = false, int blockSize = SaCommon.DefaultBlockSize)
{
_stream = writer.BaseStream;
_writer = writer;
_isPositional = isPositional;
_skipIncorrectRefEntries = skipIncorrectRefEntries;
_throwErrorOnConflicts = throwErrorOnConflicts;
_block = new NsaBlock(new Zstandard(), blockSize);
_refProvider = refProvider;
_index = new ChunkedIndex(indexWriter, refProvider.Assembly, version, jsonKey, matchByAllele, isArray, schemaVersion, isPositional);
_memBuffer = new byte[short.MaxValue * 2];
_memStream = new MemoryStream(_memBuffer);
_memWriter = new ExtendedBinaryWriter(_memStream);
}
public MitoMapVarTsvWriter(DataSourceVersion version, string outputDirectory, string mitoMapDataType, ISequenceProvider sequenceProvider)
{
Console.WriteLine(version.ToString());
_mitoMapVarWriter = new SaTsvWriter(outputDirectory, version, GenomeAssembly.rCRS.ToString(), SaTsvCommon.MitoMapSchemaVersion, mitoMapDataType, null, false, sequenceProvider, true);
}
public void ReadWriteExacDbsnp()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "2 48010488 rs1042821 G A . . RS=1042821;RSPOS=48010488;RV;dbSNPBuildID=86;SSR=0;SAO=1;VP=0x050168420a05150136100100;GENEINFO=MSH6:2956;WGT=1;VC=SNV;PM;PMC;SLO;NSM;REF;U5;R5;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;LSD;CAF=0.7991,0.2009;COMMON=1";
const string vcfLine2 =
"2 48010488 rs1042821 G A,C 14068898.15 PASS AC=21019,1;AC_AFR=1700,0;AC_AMR=1015,1;AC_Adj=19510,1;AC_EAS=1973,0;AC_FIN=743,0;AC_Het=15722,1,0;AC_Hom=1894,0;AC_NFE=10593,0;AC_OTH=147,0;AC_SAS=3339,0;AF=0.178,8.487e-06;AN=117830;AN_AFR=6388;AN_AMR=9014;AN_Adj=91130;AN_EAS=6792;AN_FIN=5078;AN_NFE=48404;AN_OTH=664;AN_SAS=14790;BaseQRankSum=-4.850e-01;ClippingRankSum=-1.400e-01;DB;DP=1206681;FS=0.000;GQ_MEAN=129.86;GQ_STDDEV=221.88;Het_AFR=1322,0,0;Het_AMR=931,1,0;Het_EAS=1511,0,0;Het_FIN=665,0,0;Het_NFE=8585,0,0;Het_OTH=111,0,0;Het_SAS=2597,0,0;Hom_AFR=189,0;Hom_AMR=42,0;Hom_EAS=231,0;Hom_FIN=39,0;Hom_NFE=1004,0;Hom_OTH=18,0;Hom_SAS=371,0;InbreedingCoeff=0.0376;MQ=60.00;MQ0=0;MQRankSum=0.00;NCC=3737;POSITIVE_TRAIN_SITE;QD=17.46;ReadPosRankSum=0.181;VQSLOD=5.87;culprit=MQ;DP_HIST=3051|9435|11318|5521|9711|11342|4131|1270|615|404|328|266|264|262|196|186|126|115|97|277,133|968|2180|3402|3564|2815|1772|954|551|389|321|263|261|261|196|186|126|115|97|277,0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=949|2966|347|492|15135|1435|1335|854|421|526|590|416|13672|1951|445|462|255|174|211|16279,24|79|81|124|135|96|110|118|97|180|228|137|182|191|126|171|180|151|192|16229,0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1";
var sa = new SupplementaryAnnotationPosition(48010488);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem1.SetSupplementaryAnnotations(saCreator);
var exacReader = new ExacReader(_renamer);
foreach (var exacItem in exacReader.ExtractItems(vcfLine2))
{
exacItem.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr2", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(48010488) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnpA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
var obsDbSnpA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
Assert.NotNull(expDbSnpA);
Assert.NotNull(obsDbSnpA);
// we want to make sure we are reading the values we have written
Assert.Equal(expDbSnpA.DbSnp, obsDbSnpA.DbSnp);
var expExacA =
sa.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacA =
observedAnnotation1.AlleleSpecificAnnotations["A"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacA);
Assert.NotNull(obsExacA);
Assert.Equal(expExacA.ExacAllAn, obsExacA.ExacAllAn);
Assert.Equal(expExacA.ExacCoverage, obsExacA.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacA.ExacAllAc), Convert.ToDouble(obsExacA.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAfrAc), Convert.ToDouble(obsExacA.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacAmrAc), Convert.ToDouble(obsExacA.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacEasAc), Convert.ToDouble(obsExacA.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacFinAc), Convert.ToDouble(obsExacA.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacNfeAc), Convert.ToDouble(obsExacA.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacOthAc), Convert.ToDouble(obsExacA.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacA.ExacSasAc), Convert.ToDouble(obsExacA.ExacSasAc));
var expExacC =
sa.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
var obsExacC =
observedAnnotation1.AlleleSpecificAnnotations["C"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Exac)] as ExacAnnotation;
Assert.NotNull(expExacC);
Assert.NotNull(obsExacC);
Assert.Equal(expExacC.ExacCoverage, obsExacC.ExacCoverage);
Assert.Equal(Convert.ToDouble(expExacC.ExacAllAc), Convert.ToDouble(obsExacC.ExacAllAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAfrAc), Convert.ToDouble(obsExacC.ExacAfrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacAmrAc), Convert.ToDouble(obsExacC.ExacAmrAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacEasAc), Convert.ToDouble(obsExacC.ExacEasAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacFinAc), Convert.ToDouble(obsExacC.ExacFinAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacNfeAc), Convert.ToDouble(obsExacC.ExacNfeAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacOthAc), Convert.ToDouble(obsExacC.ExacOthAc));
Assert.Equal(Convert.ToDouble(expExacC.ExacSasAc), Convert.ToDouble(obsExacC.ExacSasAc));
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadAndWriteDbSnp1KgEvs()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var oneKGenVersion = new DataSourceVersion("1000 Genomes Project", "phase3_shapeit2_mvncall_integrated_v5.", DateTime.Parse("2013-05-02").Ticks);
var evsDataSource = new DataSourceVersion("EVS", "V2", DateTime.Parse("2013-11-13").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, oneKGenVersion, evsDataSource
};
// create our expected supplementary annotations
const string vcfLine1 = "1 69428 rs140739101 T G . . RS=140739101;RSPOS=69428;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050200000a05140026000100;WGT=1;VC=SNV;S3D;NSM;REF;ASP;VLD;KGPhase3;CAF=0.981,0.01897;COMMON=1";
const string vcfLine2 = "1 69428 rs140739101 T G 100 PASS AC=95;AF=0.0189696;AN=5008;NS=2504;DP=17611;EAS_AF=0.003;AMR_AF=0.036;AFR_AF=0.0015;EUR_AF=0.0497;SAS_AF=0.0153;AA=.|||";
const string vcfLine3 = "1 69428 rs140739101 T G . PASS BSNP=dbSNP_134;EA_AC=313,6535;AA_AC=14,3808;TAC=327,10343;MAF=4.5707,0.3663,3.0647;GTS=GG,GT,TT;EA_GTC=92,129,3203;AA_GTC=1,12,1898;GTC=93,141,5101;DP=110;GL=OR4F5;CP=1.0;CG=0.9;AA=T;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_001005484.1:missense;HGVS_CDNA_VAR=NM_001005484.1:c.338T>G;HGVS_PROTEIN_VAR=NM_001005484.1:p.(F113C);CDS_SIZES=NM_001005484.1:918;GS=205;PH=probably-damaging:0.999;EA_AGE=.;AA_AGE=.";
const string altAllele = "G";
var sa = new SupplementaryAnnotationPosition(69428);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem = dbsnpReader.ExtractItem(vcfLine1)[0];
dbSnpItem.SetSupplementaryAnnotations(saCreator);
var oneKGenReader = new OneKGenReader(_renamer);
var oneKGenItem = oneKGenReader.ExtractItems(vcfLine2)[0];
oneKGenItem.SetSupplementaryAnnotations(saCreator);
var evsReader = new EvsReader(_renamer);
var evsItem = evsReader.ExtractItems(vcfLine3)[0];
evsItem.SetSupplementaryAnnotations(saCreator);
// the preceeding code has been unit tested in MergeDbSnp1kpEvs()
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
var observedDataSourceVersions = reader.Header.DataSourceVersions;
// check the data source versions
Assert.Equal(observedDataSourceVersions.Count, 3);
var observedDataSourceVersion = observedDataSourceVersions[0];
Assert.Equal(dbSnpVersion.Name, observedDataSourceVersion.Name);
Assert.Equal(dbSnpVersion.Version, observedDataSourceVersion.Version);
Assert.Equal(dbSnpVersion.ReleaseDateTicks, observedDataSourceVersion.ReleaseDateTicks);
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(69428) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnp =
sa.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]
as DbSnpAnnotation;
Assert.NotNull(expDbSnp);
var expOneKg =
sa.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]
as OneKGenAnnotation;
Assert.NotNull(expOneKg);
var expEvs =
sa.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]
as EvsAnnotation;
Assert.NotNull(expEvs);
var obsDbSnp = observedAnnotation1.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)]
as DbSnpAnnotation;
Assert.NotNull(obsDbSnp);
var obsOneKg = observedAnnotation1.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]
as OneKGenAnnotation;
Assert.NotNull(obsOneKg);
var obsEvs = observedAnnotation1.AlleleSpecificAnnotations[altAllele].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]
as EvsAnnotation;
Assert.NotNull(obsEvs);
Assert.Equal(expDbSnp.DbSnp, obsDbSnp.DbSnp);
Assert.Equal(expEvs.EvsAll, obsEvs.EvsAll);
Assert.Equal(expOneKg.OneKgAllAc, obsOneKg.OneKgAllAc);
Assert.Equal(expEvs.EvsCoverage, obsEvs.EvsCoverage);
Assert.Equal(expEvs.NumEvsSamples, obsEvs.NumEvsSamples);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public void ReadWriteDbSnpCosmic()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryAnnotationPosition(10229);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(saCreator)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, null);
var cosmicItem2 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(saCreator));
additionalItems.Add(cosmicItem2.SetSupplementaryAnnotations(saCreator));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
Assert.Equal(1, sa.CosmicItems.Count);
// the preceeding code has been unit tested in MergeDbSnpCosmic()
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(10229) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnp =
sa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(expDbSnp);
var obsDbSnp =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(obsDbSnp);
Assert.Equal(expDbSnp.DbSnp, obsDbSnp.DbSnp);
Assert.True(observedAnnotation1.ContainsCosmicId(sa.CosmicItems[0].ID));
Assert.Equal(1, observedAnnotation1.CosmicItems.Count);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
public ChunkedIndex(ExtendedBinaryWriter indexWriter, GenomeAssembly assembly, DataSourceVersion version, string jsonKey, bool matchByAllele, bool isArray, int schemaVersion, bool isPositional)
{
_writer = indexWriter;
MatchByAllele = matchByAllele;
JsonKey = jsonKey;
Version = version;
Assembly = assembly;
IsArray = isArray;
IsPositional = isPositional;
indexWriter.Write((byte)assembly);
version.Write(indexWriter);
indexWriter.WriteOptAscii(jsonKey);
indexWriter.Write(matchByAllele);
indexWriter.Write(isArray);
indexWriter.WriteOpt(schemaVersion);
indexWriter.Write(isPositional);
_chromChunks = new Dictionary <ushort, List <Chunk> >();
}
public void MultiAlleleMergeDbSnp1KpEvsSaRw()
{
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var oneKGenVersion = new DataSourceVersion("1000 Genomes Project", "phase3_shapeit2_mvncall_integrated_v5.", DateTime.Parse("2013-05-02").Ticks);
var evsDataSource = new DataSourceVersion("EVS", "V2", DateTime.Parse("2013-11-13").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, oneKGenVersion, evsDataSource
};
// create our expected supplementary annotations
const string vcfLine1 = "1 1564952 rs112177324 TG T . . RS=112177324;RSPOS=1564953;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x05010008000514013e000200;WGT=1;VC=DIV;SLO;INT;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.8468,0.1506;COMMON=1";
const string vcfLine2 = "1 1564952 rs112177324 TG TGG,T 100 PASS AC=13,754;AF=0.00259585,0.150559;AN=5008;NS=2504;DP=8657;EAS_AF=0,0.0933;AMR_AF=0.0014,0.2046;AFR_AF=0.0091,0.0182;EUR_AF=0,0.3588;SAS_AF=0,0.136";
const string vcfLine3 = "1 1564952 rs112177324 TG TGG,T . PASS BSNP=dbSNP_132;EA_AC=2,3039,4701;AA_AC=44,279,3231;TAC=46,3318,7932;MAF=39.2793,9.0884,29.7805;GTS=A1A1,A1A2,A1R,A2A2,A2R,RR;EA_GTC=0,1,1,707,1624,1538;AA_GTC=4,4,32,41,193,1503;GTC=4,5,33,748,1817,3041;DP=10;GL=MIB2;CP=0.8;CG=-0.0;AA=.;CA=.;EXOME_CHIP=no;GWAS_PUBMED=.;FG=NM_080875.2:intron,NM_080875.2:intron,NM_001170689.1:intron,NM_001170689.1:intron,NM_001170688.1:intron,NM_001170688.1:intron,NM_001170687.1:intron,NM_001170687.1:intron,NM_001170686.1:intron,NM_001170686.1:intron;HGVS_CDNA_VAR=NM_080875.2:c.2908+7del1,NM_080875.2:c.2908+6_2908+7insG,NM_001170689.1:c.2187-66del1,NM_001170689.1:c.2187-67_2187-66insG,NM_001170688.1:c.2713+7del1,NM_001170688.1:c.2713+6_2713+7insG,NM_001170687.1:c.2866+7del1,NM_001170687.1:c.2866+6_2866+7insG,NM_001170686.1:c.2896+7del1,NM_001170686.1:c.2896+6_28967insG;HGVS_PROTEIN_VAR=.,.,.,.,.,.,.,.,.,.;CDS_SIZES=NM_080875.2:3213,NM_080875.2:3213,NM_001170689.1:2262,NM_001170689.1:2262,NM_001170688.1:3018,NM_001170688.1:3018,NM_001170687.1:3171,NM_001170687.1:3171,NM_001170686.1:3201,NM_001170686.1:3201;GS=.,.,.,.,.,.,.,.,.,.;PH=.,.,.,.,.,.,.,.,.,.;EA_AGE=.;AA_AGE=.";
var sa = new SupplementaryAnnotationPosition(1564953);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem.SetSupplementaryAnnotations(saCreator)
};
var oneKGenReader = new OneKGenReader(_renamer);
var oneKGenItem = oneKGenReader.ExtractItems(vcfLine2)[0];
additionalItems.Add(oneKGenItem.SetSupplementaryAnnotations(saCreator));
var evsReader = new EvsReader(_renamer);
var evsItemsList = evsReader.ExtractItems(vcfLine3);
foreach (var evsItem in evsItemsList)
{
additionalItems.Add(evsItem.SetSupplementaryAnnotations(saCreator));
}
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
// write the supplementary annotation file
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
var observedDataSourceVersions = reader.Header.DataSourceVersions;
// check the data source versions
Assert.Equal(observedDataSourceVersions.Count, 3);
var observedDataSourceVersion = observedDataSourceVersions[0];
Assert.Equal(dbSnpVersion.Name, observedDataSourceVersion.Name);
Assert.Equal(dbSnpVersion.Version, observedDataSourceVersion.Version);
Assert.Equal(dbSnpVersion.ReleaseDateTicks, observedDataSourceVersion.ReleaseDateTicks);
// checking the global alleles
Assert.Null(sa.GlobalMajorAllele);
Assert.Null(sa.GlobalMajorAlleleFrequency);
Assert.Null(sa.GlobalMinorAllele);
Assert.Null(sa.GlobalMinorAlleleFrequency);
// extract the three annotations
var observedAnnotation = reader.GetAnnotation(1564953) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation);
var expectedInsOneKgAllAc = ((OneKGenAnnotation)sa.AlleleSpecificAnnotations["iG"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]).OneKgAllAc;
var expectedDelHasOneKg = sa.AlleleSpecificAnnotations["1"].HasDataSource(DataSourceCommon.DataSource.OneKg);
var expectedInsEvsAfr = ((EvsAnnotation)sa.AlleleSpecificAnnotations["iG"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]).EvsAfr;
var expectedInsHasDbSnp = sa.AlleleSpecificAnnotations["iG"].HasDataSource(DataSourceCommon.DataSource.DbSnp);
var obsAsaIns = observedAnnotation.AlleleSpecificAnnotations["iG"];
var obsAsaDel = observedAnnotation.AlleleSpecificAnnotations["1"];
Assert.Equal(expectedInsOneKgAllAc, ((OneKGenAnnotation)obsAsaIns.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)]).OneKgAllAc);
Assert.Equal(expectedDelHasOneKg, obsAsaDel.HasDataSource(DataSourceCommon.DataSource.OneKg));
Assert.Equal(expectedInsEvsAfr, ((EvsAnnotation)obsAsaIns.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.Evs)]).EvsAfr);
Assert.Equal(expectedInsHasDbSnp, obsAsaIns.HasDataSource(DataSourceCommon.DataSource.DbSnp));
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
