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 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 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 AllSuppAnnotOutputTest()
{
const string altAllele = "C";
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 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 clinvarItem1 = new ClinVarItem(null, 0, null, altAllele, null, "RCV001",
null, null, new List <string> {
"ORPHA2462"
}, null, null, "other");
sa.ClinVarItems.Add(clinvarItem1);
var saReader = new MockSupplementaryAnnotationReader(sa);
var infoColumn = VcfUtilities.GetVcfColumn(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", VcfCommon.InfoIndex);
Assert.Contains("AF1000G=0.425319", infoColumn);
Assert.Contains("cosmic=1|COSM1000,1|COSM1001", infoColumn);
Assert.Contains("clinvar=1|other", infoColumn);
}
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);
}
public void NullVcfFieldTest()
{
var sa = new SupplementaryAnnotationPosition(9580071);
var dbSnp = new DbSnpAnnotation
{
DbSnp = null
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "T", dbSnp);
var saReader = new MockSupplementaryAnnotationReader(sa);
var idColumn = VcfUtilities.GetVcfColumn(saReader,
"chr12\t9580071\t.\tA\tC,T\t394.00\tPASS\t.\tGT\t0/1", VcfCommon.IdIndex);
Assert.NotNull(idColumn);
}
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 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);
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, saReader, "chr1 115256529 . T C 1000 PASS . GT 0/1");
Assert.NotNull(annotatedVariant);
Assert.Contains("\"dbsnp\":[\"rs111\",\"rs222\",\"rs333\"]", annotatedVariant.ToString());
}