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);
}
private LiteVcfReader GetVcfReader()
{
var useStdInput = ConfigurationSettings.VcfPath == "-";
var peekStream =
new PeekStream(useStdInput
? Console.OpenStandardInput()
: FileUtilities.GetReadStream(ConfigurationSettings.VcfPath));
return(new LiteVcfReader(GZipUtilities.GetAppropriateStream(peekStream)));
}
private static AnnotationResources GetAnnotationResources()
{
var annotationResources = new AnnotationResources(_refSequencePath, _inputCachePrefix, SupplementaryAnnotationDirectories, null, _pluginDirectory, _disableRecomposition, _forceMitochondrialAnnotation);
if (SupplementaryAnnotationDirectories.Count == 0)
{
return(annotationResources);
}
using (var preloadVcfStream = GZipUtilities.GetAppropriateStream(
new PersistentStream(PersistentStreamUtils.GetReadStream(_vcfPath),
ConnectUtilities.GetFileConnectFunc(_vcfPath), 0)))
{
annotationResources.GetVariantPositions(preloadVcfStream, null);
}
return(annotationResources);
}
public void GetAppropriateStream_Handle_PeekStream()
{
string observedString;
using (var ms = new MemoryStream())
{
using (var writer = new BinaryWriter(new BlockGZipStream(ms, CompressionMode.Compress, true)))
{
writer.Write(ExpectedString);
}
ms.Position = 0;
using (var peekStream = new PeekStream(ms))
using (var reader = new BinaryReader(GZipUtilities.GetAppropriateStream(peekStream)))
{
observedString = reader.ReadString();
}
}
Assert.Equal(ExpectedString, observedString);
}
public void GetAppropriateStream_PeekStream_WithTextFile()
{
string observedString;
using (var ms = new MemoryStream())
{
using (var writer = new StreamWriter(ms, Encoding.UTF8, 1024, true))
{
writer.WriteLine(ExpectedString);
}
ms.Position = 0;
using (var peekStream = new PeekStream(ms))
using (var reader = new StreamReader(GZipUtilities.GetAppropriateStream(peekStream)))
{
observedString = reader.ReadLine();
}
}
Assert.Equal(ExpectedString, observedString);
}
private static AnnotationResources GetAnnotationResources()
{
if (_outputFileName == "-")
{
Logger.Silence();
}
var metrics = new PerformanceMetrics();
var annotationResources = new AnnotationResources(_refSequencePath, _inputCachePrefix,
SupplementaryAnnotationDirectories, null, _customStrTsv,
_disableRecomposition, _forceMitochondrialAnnotation, _useLegacyVids, metrics);
if (SupplementaryAnnotationDirectories.Count == 0)
{
return(annotationResources);
}
using (var preloadVcfStream = GZipUtilities.GetAppropriateStream(PersistentStreamUtils.GetReadStream(_vcfPath)))
{
annotationResources.GetVariantPositions(preloadVcfStream, null);
}
return(annotationResources);
}
private static GeneAnnotationsParser GetGeneAnnotationsParserFromCustomTsvStream(PersistentStream customTsvStream)
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, LambdaUrlHelper.GetUgaUrl());
return(GeneAnnotationsParser.Create(new StreamReader(GZipUtilities.GetAppropriateStream(customTsvStream)), entrezGeneIdToSymbol, ensemblGeneIdToSymbol));
}
