private static ExitCodes ProgramExecution()
{
const string tempLeftoverFilename = "LeftOvers.vcf.gz";
Dictionary <string, StreamWriter> writers;
ISequenceProvider srcSequenceProvider = ProviderUtilities.GetSequenceProvider(_srcRefSequence);
ISequenceProvider desSequenceProvider = ProviderUtilities.GetSequenceProvider(_desRefSequence);
using (var srcReader = GZipUtilities.GetAppropriateStreamReader(_srcMapFile))
using (var destReader = GZipUtilities.GetAppropriateStreamReader(_destMapFile))
using (var leftoverWriter = GZipUtilities.GetStreamWriter(tempLeftoverFilename))
{
var chromMapper = new ChromMapper(srcReader, destReader, leftoverWriter, srcSequenceProvider, desSequenceProvider);
writers = chromMapper.Map();
}
//now we will try to map the leftovers
using (var destReader = GZipUtilities.GetAppropriateStreamReader(_destMapFile))
using (var leftoverReader = GZipUtilities.GetAppropriateStreamReader(tempLeftoverFilename))
{
var leftOverMapper = new LeftoverMapper(leftoverReader, destReader, writers, desSequenceProvider);
var leftoverCount = leftOverMapper.Map();
Console.WriteLine($"{leftoverCount} leftovers mapped!!");
}
foreach (var writer in writers.Values)
{
writer.Dispose();
}
return(ExitCodes.Success);
}
public void GetNsaProvider_NoSaFile_ReturnNull()
{
var annotationFiles = new AnnotationFiles();
var nsaProvider = ProviderUtilities.GetNsaProvider(annotationFiles);
Assert.Null(nsaProvider);
}
public ValidationResult Run(ValidationConfig config, ILambdaContext context)
{
string snsTopicArn = null;
try
{
LogUtilities.UpdateLogger(context.Logger, null);
LogUtilities.LogLambdaInfo(context, CommandLineUtilities.InformationalVersion);
LogUtilities.LogObject("Config", config);
LogUtilities.Log(new[] { LambdaUrlHelper.UrlBaseEnvironmentVariableName, LambdaUtilities.SnsTopicKey });
LambdaUtilities.GarbageCollect();
snsTopicArn = LambdaUtilities.GetEnvironmentVariable(LambdaUtilities.SnsTopicKey);
config.Validate();
GenomeAssembly genomeAssembly = GenomeAssemblyHelper.Convert(config.genomeAssembly);
string nirvanaS3Ref = LambdaUrlHelper.GetRefUrl(genomeAssembly);
var refProvider = ProviderUtilities.GetSequenceProvider(nirvanaS3Ref);
using (var stream = PersistentStreamUtils.GetReadStream(config.customStrUrl))
TryLoadStrFile(stream, genomeAssembly, refProvider);
}
catch (Exception exception)
{
return(HandleException(config.id, exception, snsTopicArn));
}
return(GetSuccessOutput(config.id));
}
private static (Annotator Annotator, IDictionary <string, IChromosome> RefNames) GetAnnotatorAndReferenceDict(string cacheFilePrefix, List <string> saPaths)
{
var sequenceFilePath = cacheFilePrefix + ".bases";
var sequenceProvider = ProviderUtilities.GetSequenceProvider(sequenceFilePath);
var refNames = sequenceProvider.RefNameToChromosome;
var transcriptAnnotationProvider = ProviderUtilities.GetTranscriptAnnotationProvider(cacheFilePrefix, sequenceProvider);
var saProvider = ProviderUtilities.GetSaProvider(saPaths);
var conservationProvider = ProviderUtilities.GetConservationProvider(saPaths);
var annotator = new Annotator(transcriptAnnotationProvider, sequenceProvider, saProvider, conservationProvider, null);
return(annotator, refNames);
}
private static (Annotator Annotator, ISequenceProvider SequenceProvider) GetAnnotatorAndSequenceProvider(string cacheFilePrefix, List <string> saPaths)
{
var annotationFiles = new AnnotationFiles();
saPaths?.ForEach(x => annotationFiles.AddFiles(x));
var sequenceFilePath = cacheFilePrefix + ".bases";
var sequenceProvider = ProviderUtilities.GetSequenceProvider(sequenceFilePath);
var transcriptAnnotationProvider = ProviderUtilities.GetTranscriptAnnotationProvider(cacheFilePrefix, sequenceProvider);
var saProvider = ProviderUtilities.GetNsaProvider(annotationFiles);
var conservationProvider = ProviderUtilities.GetConservationProvider(annotationFiles);
var annotator = new Annotator(transcriptAnnotationProvider, sequenceProvider, saProvider, conservationProvider, null);
return(annotator, sequenceProvider);
}
internal static IAnnotatedPosition GetAnnotatedPosition(string cacheFilePrefix, List <string> saPaths,
string vcfLine, bool enableVerboseTranscripts)
{
var refMinorProvider = ProviderUtilities.GetRefMinorProvider(saPaths);
var annotatorAndRef = GetAnnotatorAndReferenceDict(cacheFilePrefix, saPaths);
var annotator = annotatorAndRef.Annotator;
var refNames = annotatorAndRef.RefNames;
var variantFactory = new VariantFactory(refNames, refMinorProvider, enableVerboseTranscripts);
var position = VcfReaderUtils.ParseVcfLine(vcfLine, variantFactory, refNames);
var annotatedPosition = annotator.Annotate(position);
return(annotatedPosition);
}
internal static IAnnotatedPosition GetAnnotatedPosition(string cacheFilePrefix, List <string> saPaths,
string vcfLine)
{
var annotationFiles = new AnnotationFiles();
saPaths?.ForEach(x => annotationFiles.AddFiles(x));
var refMinorProvider = ProviderUtilities.GetRefMinorProvider(annotationFiles);
var(annotator, sequenceProvider) = GetAnnotatorAndSequenceProvider(cacheFilePrefix, saPaths);
var variantFactory = new VariantFactory(sequenceProvider);
var position = ParseVcfLine(vcfLine, refMinorProvider, variantFactory, sequenceProvider.RefNameToChromosome);
var annotatedPosition = annotator.Annotate(position);
return(annotatedPosition);
}
public void SqlCeSchemaShouldBeGeneratedAndUsable()
{
var recordDescriptors = new[] {
new RecordBlueprint {
TableName = "Hello", Type = typeof(FooRecord)
}
};
ProviderUtilities.RunWithSqlCe(recordDescriptors,
sessionFactory => {
var session = sessionFactory.OpenSession();
var foo = new FooRecord {
Name = "hi there"
};
session.Save(foo);
session.Flush();
session.Close();
Assert.That(foo, Is.Not.EqualTo(0));
});
}
public void SqlServerSchemaShouldBeGeneratedAndUsable()
{
var recordDescriptors = new[] {
new RecordBlueprint {
TableName = "Hello", Type = typeof(FooRecord)
}
};
ProviderUtilities.RunWithSqlServer(recordDescriptors,
sessionFactory => {
var session = sessionFactory.OpenSession();
var foo = new FooRecord {
Name = "hi there", Timespan = DateTime.Now
};
session.Insert(foo);
//session.Flush();
session.Close();
Assert.NotEqual(foo.Id, default(int));
});
}
