public static void FieldDoesNotContain(ISupplementaryAnnotationReader saReader,
string vcfLine, string expected, int vcfColumn)
{
var column = GetVcfColumn(saReader, vcfLine, vcfColumn);
Assert.DoesNotContain(expected, column);
}
internal static IAnnotatedVariant GetVariant(string cacheFile, ISupplementaryAnnotationReader saReader,
string vcfLine)
{
var annotationSource = ResourceUtilities.GetAnnotationSource(cacheFile, saReader);
return(GetVariant(annotationSource, vcfLine));
}
public static void FieldEquals(ISupplementaryAnnotationReader saReader, string vcfLine,
string expected, int vcfColumn)
{
var column = GetVcfColumn(saReader, vcfLine, vcfColumn);
Assert.Equal(expected, column);
}
internal static IAnnotatedVariant GetVariant(string cachePath, ISupplementaryAnnotationReader saReader,
string vcfLine, IConservationScoreReader csReader)
{
var annotationSource = ResourceUtilities.GetAnnotationSource(cachePath, saReader, csReader);
return(GetVariant(annotationSource, vcfLine));
}
/// <summary>
/// constructor
/// </summary>
public MockSupplementaryAnnotationProvider(ISupplementaryAnnotationReader saReader, ChromosomeRenamer renamer)
{
if (saReader == null)
{
return;
}
_saReader = saReader;
_overlappingSupplementaryIntervals = new List <ISupplementaryInterval>();
_suppIntervalForest = _saReader.GetIntervalForest(renamer);
}
/// <summary>
/// creates a new annotation source with data from the micro-cache file
/// </summary>
internal static IAnnotationSource GetAnnotationSource(string cachePath, ISupplementaryAnnotationReader saReader,
IConservationScoreReader conservationScoreReader = null,
ISupplementaryAnnotationProvider customAnnotationProvider = null,
ISupplementaryAnnotationProvider customIntervalProvider = null)
{
var streams = GetAnnotationSourceStreams(cachePath);
var renamer = ChromosomeRenamer.GetChromosomeRenamer(GetReadStream($"{cachePath}.bases"));
var saProvider = new MockSupplementaryAnnotationProvider(saReader, renamer);
PerformanceMetrics.DisableOutput = true;
return(new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader, customAnnotationProvider,
customIntervalProvider, null));
}
/// <summary>
/// sets the supplementary annotation record for each allele in this record
/// </summary>
public void SetSupplementaryAnnotation(ISupplementaryAnnotationReader saReader)
{
// for ref variants, alternate alleles will be empty. We will need to pull the SA from reference position.
// If this is a ref minor position, I will add an alt allele with the ref as alt and GMAF as ref
if (IsReference)
{
// checking the index for refMinor using the index before actually going to disk
IsRefMinor = saReader.IsRefMinor(VcfReferenceBegin);
if (!IsRefMinor)
{
return;
}
SupplementaryAnnotationPosition = saReader.GetAnnotation(VcfReferenceBegin);
if (SupplementaryAnnotationPosition == null)
{
return;
}
// if we have a ref minor, we do not care about ref no call
IsRefNoCall = false;
AlternateAlleles[0].AlternateAllele = AlternateAlleles[0].ReferenceAllele;// ref becomes alt for ref minor
if (SupplementaryAnnotationPosition.GlobalMajorAllele != null)
{
AlternateAlleles[0].ReferenceAllele = SupplementaryAnnotationPosition.GlobalMajorAllele;
}
AlternateAlleles[0].NirvanaVariantType = VariantType.SNV;
AlternateAlleles[0].VepVariantType = VariantType.SNV;
AlternateAlleles[0].SuppAltAllele = AlternateAlleles[0].AlternateAllele; // for SNVs there is nothing to reduce
AlternateAlleles[0].VariantId = _vid.Create(_renamer, EnsemblReferenceName, AlternateAlleles[0]);
AlternateAlleles[0].SetSupplementaryAnnotation(SupplementaryAnnotationPosition);
return;
}
foreach (var altAllele in AlternateAlleles)
{
var sa = saReader.GetAnnotation(altAllele.Start);
if (sa != null)
{
altAllele.SetSupplementaryAnnotation(sa);
}
}
}
public static string GetVcfColumn(ISupplementaryAnnotationReader saReader, string vcfLine,
int vcfColumn)
{
var vcfVariant = GetVcfVariant(vcfLine);
var annotationSource = ResourceUtilities.GetAnnotationSource(DataUtilities.EmptyCachePrefix, saReader);
UnifiedJson.NeedsVariantComma = false;
var annotatedVariant = annotationSource?.Annotate(vcfVariant);
Assert.NotNull(annotatedVariant);
var vcf = new VcfConversion();
return(vcf.Convert(vcfVariant, annotatedVariant).Split('\t')[vcfColumn]);
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
if (string.IsNullOrEmpty(_saDir) || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
var saPath = Path.Combine(_saDir, ucscReferenceName + ".nsa");
_saReader = File.Exists(saPath) ? new SupplementaryAnnotationReader(saPath) : null;
_intervalForest = _saReader?.GetIntervalForest(renamer);
_hasIntervals = !(_intervalForest is NullIntervalSearch <ISupplementaryInterval>);
_currentUcscReferenceName = ucscReferenceName;
}
public void Clear() => _saReader = null;
public void Clear()
{
_hasIntervals = false;
_saReader = null;
}