private IAnnotationProvider GetClinVarProvider()
{
var chrom1Pos100Annotations = new List <(string refAllele, string altAllele, string annotation)>
{
("A", "T", "RCV00001"),
("A", "C", "RCV00002")
};
var clinvarReader = new Mock <INsaReader>();
clinvarReader.SetupGet(x => x.Assembly).Returns(GenomeAssembly.GRCh37);
clinvarReader.SetupGet(x => x.MatchByAllele).Returns(false);
clinvarReader.SetupGet(x => x.IsArray).Returns(true);
clinvarReader.SetupGet(x => x.JsonKey).Returns("clinvar");
clinvarReader.SetupGet(x => x.Version)
.Returns(new DataSourceVersion("clinvar", "v1", DateTime.Now.Ticks, "dummy clinvar data"));
clinvarReader.SetupSequence(x => x.GetAnnotation(100)).Returns(chrom1Pos100Annotations);
var provider = new NsaProvider(new[] { clinvarReader.Object }, null);
return(provider);
}
private IAnnotationProvider GetDbSnpProvider()
{
var chrom1Pos100Annotations = new List <(string refAllele, string altAllele, string annotation)>
{
("A", "T", "\"rs100\""),
("A", "C", "\"rs101\"")
};
var dbsnpReader = new Mock <INsaReader>();
dbsnpReader.SetupGet(x => x.Assembly).Returns(GenomeAssembly.GRCh37);
dbsnpReader.SetupGet(x => x.MatchByAllele).Returns(true);
dbsnpReader.SetupGet(x => x.IsArray).Returns(true);
dbsnpReader.SetupGet(x => x.JsonKey).Returns("dbSnp");
dbsnpReader.SetupGet(x => x.Version)
.Returns(new DataSourceVersion("dbsnp", "v1", DateTime.Now.Ticks, "dummy db snp"));
dbsnpReader.SetupSequence(x => x.GetAnnotation(100)).Returns(chrom1Pos100Annotations);
var provider = new NsaProvider(new[] { dbsnpReader.Object }, null);
return(provider);
}
