public IEnumerable <ISupplementaryInterval> GetSupplementaryIntervals(IChromosomeRenamer renamer)
{
if (_intervalsPosition == -1)
{
return(null);
}
var returnPosition = _stream.Position;
_stream.Position = _intervalsPosition;
var count = _reader.ReadInt32(); // how many supplementary intervals to read
if (count == 0)
{
return(null);
}
var intervalList = new List <SupplementaryInterval>(count);
for (var i = 0; i < count; i++)
{
intervalList.Add(SupplementaryInterval.Read(_reader, renamer));
}
_stream.Position = returnPosition;
return(intervalList);
}
/// <summary>
/// constructor
/// </summary>
public SaReadWriteTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
_sequence = fixture.Sequence;
_reader = fixture.Reader;
// create our expected data source versions
_expectedDataSourceVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
_expectedDataSourceVersions = new List <DataSourceVersion> {
_expectedDataSourceVersion
};
// create our expected supplementary annotations
var dbSnp1 = new DbSnpAnnotation
{
DbSnp = new List <long> {
1
}
};
_expectedAnnotation1 = new SupplementaryAnnotationPosition(100);
new SupplementaryPositionCreator(_expectedAnnotation1).AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, AltAllele, dbSnp1);
var dbSnp2 = new DbSnpAnnotation
{
DbSnp = new List <long> {
2
}
};
_expectedAnnotation2 = new SupplementaryAnnotationPosition(101);
new SupplementaryPositionCreator(_expectedAnnotation2).AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, AltAllele, dbSnp2);
var dbSnp3 = new DbSnpAnnotation
{
DbSnp = new List <long> {
3
}
};
_expectedAnnotation3 = new SupplementaryAnnotationPosition(102);
new SupplementaryPositionCreator(_expectedAnnotation3).AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, AltAllele, dbSnp3);
_expectedInterval = new SupplementaryInterval(1, 1000, "chr1", null, VariantType.copy_number_variation, null, _renamer);
_randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// write the supplementary annotation file
WriteSupplementaryAnnotationFile(_randomPath);
}
public override SupplementaryInterval GetSupplementaryInterval(ChromosomeRenamer renamer)
{
if (!IsInterval)
{
return(null);
}
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 stringLists = new Dictionary <string, IEnumerable <string> >();
var suppInterval = new SupplementaryInterval(Start, End, Chromosome, null, VariantType,
"ClinGen", renamer, intValues, doubleValues, freqValues, stringValues, boolValues, stringLists);
if (Id != null)
{
suppInterval.AddStringValue("id", Id);
}
if (ClinicalInterpretation != ClinicalInterpretation.unknown)
{
suppInterval.AddStringValue("clinicalInterpretation", GetClinicalDescription(ClinicalInterpretation));
}
if (Phenotypes != null)
{
suppInterval.AddStringList("phenotypes", Phenotypes);
}
if (PhenotypeIds != null)
{
suppInterval.AddStringList("phenotypeIds", PhenotypeIds);
}
if (ObservedGains != 0)
{
suppInterval.AddIntValue("observedGains", ObservedGains);
}
if (ObservedLosses != 0)
{
suppInterval.AddIntValue("observedLosses", ObservedLosses);
}
if (Validated)
{
suppInterval.AddBoolValue("validated");
}
return(suppInterval);
}
public override SupplementaryInterval GetSupplementaryInterval(ChromosomeRenamer renamer)
{
if (!IsInterval)
{
return(null);
}
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(Start, End, Chromosome, null, VariantType,
"DGV", renamer, intValues, doubleValues, freqValues, stringValues, boolValues);
if (Id != null)
{
suppInterval.AddStringValue("id", Id);
}
if (SampleSize != 0)
{
suppInterval.AddIntValue("sampleSize", SampleSize);
}
if (ObservedGains != 0)
{
suppInterval.AddIntValue("observedGains", ObservedGains);
}
if (ObservedLosses != 0)
{
suppInterval.AddIntValue("observedLosses", ObservedLosses);
}
if (VariantFreqAll != null)
{
suppInterval.AddFrequencyValue("variantFreqAll", VariantFreqAll.Value);
}
return(suppInterval);
}
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 override SupplementaryInterval GetSupplementaryInterval(ChromosomeRenamer renamer)
{
if (!IsInterval)
{
return(null);
}
var seqAltType = SequenceAlterationUtilities.GetSequenceAlteration(SvType, ObservedGains, ObservedLosses);
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(Start, SvEnd, Chromosome, AlternateAllele, seqAltType,
"1000 Genomes Project", renamer, intValues, doubleValues, freqValues, stringValues, boolValues);
if (Id != null)
{
suppInterval.AddStringValue("id", Id);
}
if (AfrFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqAfr", Convert.ToDouble(AfrFreq));
}
if (AllFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqAll", Convert.ToDouble(AllFreq));
}
if (AmrFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqAmr", Convert.ToDouble(AmrFreq));
}
if (EasFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqEas", Convert.ToDouble(EasFreq));
}
if (EurFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqEur", Convert.ToDouble(EurFreq));
}
if (SasFreq != null)
{
suppInterval.AddFrequencyValue("variantFreqSas", Convert.ToDouble(SasFreq));
}
if (AllAlleleNumber != null && AllAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSize", AllAlleleNumber.Value);
}
if (AfrAlleleNumber != null && AfrAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeAfr", AfrAlleleNumber.Value);
}
if (AmrAlleleNumber != null && AmrAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeAmr", AmrAlleleNumber.Value);
}
if (EasAlleleNumber != null && EasAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeEas", EasAlleleNumber.Value);
}
if (EurAlleleNumber != null && EurAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeEur", EurAlleleNumber.Value);
}
if (SasAlleleNumber != null && SasAlleleNumber.Value > 0)
{
suppInterval.AddIntValue("sampleSizeSas", SasAlleleNumber.Value);
}
if (ObservedGains != 0)
{
suppInterval.AddIntValue("observedGains", ObservedGains);
}
if (ObservedLosses != 0)
{
suppInterval.AddIntValue("observedLosses", ObservedLosses);
}
return(suppInterval);
}
