public void ClinvarSignificanceWithComma()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chrX_76937963_76937963.nsa"));
VcfUtilities.FieldContains(saReader, "X 76937963 . G C . . .",
"conflicting_interpretations_of_pathogenicity\\x2c_not_provided", VcfCommon.InfoIndex);
}
public void DbSnpOutputTest()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr1_115256529_115256530.nsa"));
VcfUtilities.FieldContains(saReader,
"chr1 115256529 . T C 1000 PASS . GT 0/1", "rs11554290", VcfCommon.IdIndex);
}
public void OneAlleleFreqMissing()
{
var sa = new SupplementaryAnnotationPosition(825069);
var saCreator = new SupplementaryPositionCreator(sa);
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
4475692
}
};
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 3392
};
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1 825069 rs4475692 G A,C 362.00 LowGQX;HighDPFRatio SNVSB=-36.9;SNVHPOL=3 GT:GQ:GQX:DP:DPF:AD 1/2:4:0:52:38:8,11,33",
"AF1000G=.,0.677316", VcfCommon.InfoIndex);
}
public void UnwantedRefMinor()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnotGRCh38("chr1_26213904_26213905.nsa"));
VcfUtilities.FieldContains(saReader,
"chr1 26213904 . C . . LowGQX;HighDPFRatio . GT:GQX:DP:DPF 0/0:3:1:1", "RefMinor", VcfCommon.InfoIndex);
}
public void EvsOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
121913237
}
};
var evs = new EvsAnnotation
{
EvsAll = "0.0001",
EvsCoverage = "102",
NumEvsSamples = "3456"
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.Evs, "C", evs);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "EVS=0.0001|102|3456", VcfCommon.InfoIndex);
}
public void AlleleFrequency1KgOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 2130,
OneKgAmrAn = 694,
OneKgAmrAc = 250
};
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11554290
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "AF1000G=0.425319", VcfCommon.InfoIndex);
}
public void CosmicOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var saCreator = new SupplementaryPositionCreator(sa);
var altAllele = "C";
var cosmicItem1 = new CosmicItem("chr1", 115256529, "COSM1000", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, 1,
altAllele);
var cosmicItem2 = new CosmicItem("chr1", 115256529, "COSM1001", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, 1,
altAllele);
cosmicItem1.AddCosmicToSa(saCreator);
cosmicItem2.AddCosmicToSa(saCreator);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "cosmic=1|COSM1000", VcfCommon.InfoIndex);
}
public void ClinVarOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var clinvarItem1 = new ClinVarItem(null, 0, null, "C", null, "RCV001",
null, null, new List <string> {
"ORPHA2462"
}, null, null, "other");
sa.ClinVarItems.Add(clinvarItem1);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "clinvar=1|other", VcfCommon.InfoIndex);
}
public void DbSnpOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11554290
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "rs11554290", VcfCommon.IdIndex);
}
public void MultipleDbSnpIds()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
111, 222, 333
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\tMantaFluff\tT\tC\t1000\tPASS\t.\tGT\t0/1", "MantaFluff;rs111;rs222;rs333",
VcfCommon.IdIndex);
}
public void MultiAlleleTest()
{
var sa = new SupplementaryAnnotationPosition(4634317);
var oneKg1 = new OneKGenAnnotation
{
AncestralAllele = "C",
OneKgAllAn = 5008,
OneKgAllAc = 2049
};
var oneKg2 = new OneKGenAnnotation
{
AncestralAllele = "C",
OneKgAllAn = 5008,
OneKgAllAc = 1200
};
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11078537
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "A", dbSnp);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "T", dbSnp);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "A", oneKg1);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "T", oneKg2);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"17\t4634317\trs11078537\tC\tA,T\t256\tPASS\t.\tGT\t0/1", "AF1000G=0.409145,0.239617", VcfCommon.InfoIndex);
}