public void GetNotation_tests(int start, int end, string referenceAllele, string altAllele, VariantType type, string expectedHgvsg)
{
var simpleVariant = new SimpleVariant(null, start, end, referenceAllele, altAllele, type);
var observedHgvsg = HgvsgNotation.GetNotation(ReferenceAssertion, simpleVariant, SimpleSequence, _referenceInterval);
Assert.Equal(expectedHgvsg, observedHgvsg);
}
/// <summary>
/// returns true if the specified reference sequence is in the standard reference sequences and in VEP
/// </summary>
public void Annotate(IAnnotatedPosition annotatedPosition)
{
LoadChromosome(annotatedPosition.Position.Chromosome);
if (annotatedPosition.AnnotatedVariants == null)
{
return;
}
annotatedPosition.CytogeneticBand = _cytogeneticBands.GetCytogeneticBand(annotatedPosition.Position.Chromosome, annotatedPosition.Position.Start,
annotatedPosition.Position.End);
if (annotatedPosition.Position.Chromosome.UcscName != "chrM")
{
return;
}
const string assertionNumber = "NC_012920.1";
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
annotatedVariant.HgvsgNotation = HgvsgNotation.GetNotation(assertionNumber, annotatedVariant.Variant, Sequence, new Interval(0, Sequence.Length));
}
}
public void Annotate(IAnnotatedPosition annotatedPosition)
{
if (annotatedPosition.AnnotatedVariants == null)
{
return;
}
annotatedPosition.CytogeneticBand = Sequence.CytogeneticBands.Find(annotatedPosition.Position.Chromosome, annotatedPosition.Position.Start,
annotatedPosition.Position.End);
// we don't want HGVS g. nomenclature for structural variants or STRs
if (annotatedPosition.Position.HasStructuralVariant || annotatedPosition.Position.HasShortTandemRepeat)
{
return;
}
string refSeqAccession = annotatedPosition.Position.Chromosome.RefSeqAccession;
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
annotatedVariant.HgvsgNotation = HgvsgNotation.GetNotation(refSeqAccession, annotatedVariant.Variant, Sequence, new Interval(0, Sequence.Length));
}
}
