private void UpdateKnownPriors()
{
if (!string.IsNullOrEmpty(_options.PriorsPath))
{
using (var reader = new AlleleReader(_options.PriorsPath))
{
_knownVariants = reader.GetVariantsByChromosome(true, true, new List <AlleleCategory> {
AlleleCategory.Insertion, AlleleCategory.Mnv
}, doSkipCandidate: SkipPrior);
if (_options.TrimMnvPriors)
{
foreach (var knownVariantList in _knownVariants.Values)
{
foreach (var knownVariant in knownVariantList)
{
if (knownVariant.Type == AlleleCategory.Mnv)
{
knownVariant.ReferenceAllele = knownVariant.ReferenceAllele.Substring(1);
knownVariant.AlternateAllele = knownVariant.AlternateAllele.Substring(1);
knownVariant.ReferencePosition++;
}
}
}
}
}
}
}
public void GetVariantsByChromosome()
{
var vcfReader =
new AlleleReader(Path.Combine(TestPaths.LocalTestDataDirectory, "VcfReader_Extensions.vcf"));
//Simple case
var output = vcfReader.GetVariantsByChromosome(true, true,
new List <AlleleCategory> {
AlleleCategory.Insertion, AlleleCategory.Mnv
});
Assert.Equal(1, output.Count);
Assert.True(output.ContainsKey("chr1"));
var candidateAlleles = new List <CandidateAllele>();
output.TryGetValue("chr1", out candidateAlleles);
Assert.Equal(2, candidateAlleles.Count);
Assert.Equal(AlleleCategory.Mnv, candidateAlleles[0].Type);
Assert.Equal(AlleleCategory.Insertion, candidateAlleles[1].Type);
//Custom rule
var filteredVcfReader =
new AlleleReader(Path.Combine(TestPaths.LocalTestDataDirectory, "VcfReader_Extensions.vcf"));
var filteredOutput = filteredVcfReader.GetVariantsByChromosome(true, true,
new List <AlleleCategory> {
AlleleCategory.Insertion, AlleleCategory.Mnv
}, candidate => candidate.ReferenceAllele.Length > 3);
Assert.Equal(1, filteredOutput.Count);
Assert.True(filteredOutput.ContainsKey("chr1"));
var filteredCandidateAlleles = new List <CandidateAllele>();
filteredOutput.TryGetValue("chr1", out filteredCandidateAlleles);
Assert.Equal(1, filteredCandidateAlleles.Count);
Assert.False(filteredCandidateAlleles.Any(c => c.ReferenceAllele.Length > 3));
}