public void DeletionWithoutSymbolicAllele()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000257290_chr4_Ensembl84"),
"1 823830 . AGAGAAGGAGAGAAGGAAGGAAGGAGGGAGAGAAAGGGAAAGAAGGAAAGAAACAAGGAAGCAGGGAGGGAGAGAAAGAGGAAGGGAG A 495 MaxDepth;MaxMQ0Frac END=823917;SVTYPE=DEL;SVLEN=-87;CIGAR=1M87D;ColocalizedCanvas GT:GQ:PR:SR 0/1:495:80,0:93,25");
var observedJsonLine = JsonUtilities.GetFirstAlleleJson(annotatedVariant);
const string expectedJsonLine = "{\"altAllele\":\"-\",\"refAllele\":\"GAGAAGGAGAGAAGGAAGGAAGGAGGGAGAGAAAGGGAAAGAAGGAAAGAAACAAGGAAGCAGGGAGGGAGAGAAAGAGGAAGGGAG\",\"begin\":823831,\"chromosome\":\"1\",\"end\":823917,\"variantType\":\"deletion\",\"vid\":\"1:823831:823917\"}";
Assert.Equal(expectedJsonLine, observedJsonLine);
}
public void BasicCustomIntervalOutput()
{
var customIntervalProvider = new MockCustomIntervalProvider(ResourceUtilities.GetReadStream(Resources.CustomIntervals("chr1_IcslIntervals_69090_69091.nci")), _renamer);
var annotationSource = ResourceUtilities.GetAnnotationSource(DataUtilities.EmptyCachePrefix, null, null, customIntervalProvider);
var annotatedVariant = DataUtilities.GetVariant(annotationSource,
"chr1 69092 . T C . LowGQX;HighDPFRatio END=10244;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:1");
Assert.NotNull(annotatedVariant);
const string expectedJson = "{\"altAllele\":\"C\",\"refAllele\":\"T\",\"begin\":69092,\"chromosome\":\"chr1\",\"end\":69092,\"variantType\":\"SNV\",\"vid\":\"1:69092:C\",\"IcslIntervals\":[{\"Start\":69091,\"End\":70008,\"gene\":\"OR4F5\",\"assesment\":\"Some_evidence_of_constraint\",\"score\":0.0,\"exacScore\":3.60208899915}]}";
var observedJson = JsonUtilities.GetFirstAlleleJson(annotatedVariant);
Assert.Equal(expectedJson, observedJson);
}
public void AnnotationCarryover()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr2_90472571_90472592.nsa"),
"2 90472571 . AAAAAAAAAAAAAAAAAAGTCC AGTCT 177 PASS CIGAR=1M21D4I;RU=.;REFREP=.;IDREP=. GT:GQ:GQX:DPI:AD 0/1:220:177:46:40,7");
Assert.NotNull(annotatedVariant);
var altAllele = JsonUtilities.GetFirstAlleleJson(annotatedVariant);
Assert.NotNull(altAllele);
Assert.Equal("{\"altAllele\":\"GTCT\",\"refAllele\":\"AAAAAAAAAAAAAAAAAGTCC\",\"begin\":90472572,\"chromosome\":\"2\",\"end\":90472592,\"variantType\":\"indel\",\"vid\":\"2:90472572:90472592:GTCT\"}", altAllele);
var annotatedVariant2 = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr2_90472571_90472592.nsa"),
"2 90472592 . C . . PASS RefMinor GT:GQX:DP:DPF:AD 0:96:33:15:33");
Assert.NotNull(annotatedVariant2);
var altAllele2 = JsonUtilities.GetFirstAlleleJson(annotatedVariant2);
Assert.NotNull(altAllele2);
Assert.Equal("{\"refAllele\":\"C\",\"begin\":90472592,\"chromosome\":\"2\",\"end\":90472592,\"globalMinorAllele\":\"C\",\"gmaf\":0.006989,\"isReferenceMinorAllele\":true,\"variantType\":\"SNV\",\"vid\":\"2:90472592:C\"}", altAllele2);
}
